Pipeline Report

Created by Bpipe, Mon May 16 11:59:17 EST 2016


Result


Succeeded

Timeline


16.007 s
2.911 s
21.131 s
0.841 s
23.009 s
22.287 s
1.301 s
1.811 s
1.109 s
1.087 s
2.174 s
0.989 s
0.889 s
3.651 s
2 mins, 31.072 s
0.035 s
0.008 s
20.274 s
1.125 s
21.963 s
1.419 s
25.610 s
23.637 s
0.838 s
0.807 s
0.965 s
0.745 s
1.252 s
1.156 s
2.621 s
26.807 s
17 mins, 55.226 s
0.043 s
0.012 s
20.284 s
0.798 s
21.106 s
1.318 s
22.794 s
26.739 s
0.644 s
0.740 s
0.717 s
0.730 s
0.800 s
0.308 s
1.029 s
22.311 s
3 mins, 50.415 s
0.053 s
0.008 s
20.903 s
0.890 s
22.570 s
0.972 s
25.277 s
23.294 s
0.745 s
0.658 s
0.675 s
0.775 s
1.437 s
0.986 s
0.919 s
24.174 s
5 mins, 34.706 s
0.052 s
0.013 s
19.946 s
1.279 s
22.714 s
1.584 s
24.368 s
23.851 s
0.685 s
0.709 s
0.731 s
0.729 s
0.471 s
0.821 s
1.083 s
23.669 s
8 mins, 25.317 s
0.035 s
0.009 s
20.752 s
1.203 s
22.884 s
1.299 s
25.114 s
23.000 s
0.725 s
0.924 s
0.849 s
0.752 s
1.136 s
1.249 s
1.883 s
28.291 s
16 mins, 35.496 s
0.032 s
0.007 s
20.731 s
0.773 s
21.627 s
1.298 s
24.831 s
24.487 s
0.691 s
0.725 s
0.710 s
1.028 s
1.121 s
0.955 s
1.115 s
25.812 s
12 mins, 27.021 s
0.036 s
0.008 s
20.253 s
1.177 s
22.602 s
0.971 s
24.710 s
24.289 s
0.748 s
0.696 s
0.935 s
1.027 s
1.114 s
1.442 s
2.035 s
29.399 s
19 mins, 2.280 s
0.037 s
0.009 s
21.333 s
1.634 s
23.016 s
1.215 s
23.476 s
23.241 s
0.871 s
0.769 s
0.629 s
0.737 s
1.153 s
1.186 s
1.022 s
26.432 s
9 mins, 52.736 s
0.032 s
0.008 s
20.769 s
1.034 s
22.426 s
1.053 s
24.714 s
23.988 s
0.789 s
0.664 s
0.701 s
0.985 s
1.458 s
0.855 s
2.114 s
27.275 s
18 mins, 34.704 s
0.034 s
0.009 s
14.577 s
0.101 s
18.801 s
4.837 s
22.930 s
25.989 s
2.014 s
1.794 s
1.229 s
1.446 s
1.209 s
1.250 s
0.677 s
14.783 s
3 mins, 0.645 s
0.034 s
0.009 s
20.663 s
1.204 s
21.862 s
1.504 s
27.131 s
22.614 s
0.832 s
0.731 s
1.028 s
0.945 s
1.239 s
2.446 s
2.446 s
25.791 s
20 mins, 9.177 s
0.035 s
0.008 s
20.237 s
1.157 s
21.543 s
1.310 s
25.146 s
24.264 s
0.757 s
0.828 s
0.699 s
0.845 s
0.907 s
0.926 s
1.089 s
27.209 s
13 mins, 55.857 s
0.034 s
0.008 s
20.601 s
0.824 s
21.611 s
1.602 s
23.048 s
24.521 s
0.963 s
0.741 s
0.959 s
0.688 s
1.173 s
0.979 s
1.155 s
24.410 s
6 mins, 13.767 s
0.037 s
0.010 s
19.791 s
1.107 s
22.484 s
1.122 s
24.531 s
22.909 s
1.457 s
0.714 s
0.833 s
0.770 s
0.821 s
0.538 s
1.083 s
22.487 s
3 mins, 48.733 s
0.038 s
0.008 s
20.585 s
0.782 s
24.768 s
2.330 s
23.849 s
21.821 s
0.794 s
0.532 s
0.803 s
0.870 s
1.168 s
0.941 s
1.657 s
24.641 s
13 mins, 42.721 s
0.052 s
0.012 s
20.582 s
0.945 s
23.261 s
1.778 s
25.667 s
22.278 s
0.743 s
0.727 s
0.812 s
0.623 s
0.778 s
1.273 s
2.605 s
26.728 s
12 mins, 46.603 s
0.031 s
0.007 s
20.245 s
0.855 s
22.781 s
1.835 s
26.828 s
22.839 s
0.654 s
0.549 s
0.405 s
0.927 s
1.006 s
1.809 s
1.892 s
26.708 s
13 mins, 11.583 s
0.032 s
0.010 s
20.375 s
0.978 s
23.168 s
1.186 s
25.584 s
23.525 s
0.886 s
0.814 s
0.816 s
1.082 s
1.148 s
2.016 s
3.346 s
27.661 s
19 mins, 13.539 s
0.031 s
0.007 s
20.528 s
1.270 s
22.406 s
1.090 s
23.404 s
24.600 s
1.044 s
0.599 s
0.834 s
0.995 s
0.990 s
0.969 s
1.134 s
26.124 s
11 mins, 12.865 s
0.064 s
0.013 s
20.436 s
0.786 s
22.090 s
1.711 s
26.300 s
22.944 s
0.676 s
0.709 s
0.561 s
0.648 s
1.111 s
1.036 s
0.874 s
26.241 s
8 mins, 43.490 s
0.035 s
0.009 s
21.623 s
2.680 s
21.079 s
1.158 s
24.114 s
24.231 s
0.814 s
0.769 s
0.618 s
0.429 s
1.269 s
0.835 s
1.320 s
27.764 s
14 mins, 1.990 s
0.052 s
0.013 s
20.787 s
1.905 s
21.837 s
1.100 s
24.413 s
23.556 s
0.576 s
0.629 s
0.573 s
0.980 s
0.914 s
1.152 s
0.873 s
24.287 s
5 mins, 41.153 s
0.041 s
0.008 s
21.243 s
1.216 s
22.098 s
0.892 s
24.097 s
24.433 s
0.795 s
0.913 s
0.897 s
0.362 s
1.333 s
0.926 s
2.849 s
25.047 s
13 mins, 40.936 s
0.032 s
0.012 s
21.330 s
1.518 s
22.160 s
1.350 s
24.356 s
22.919 s
0.786 s
0.623 s
0.669 s
0.871 s
0.868 s
1.261 s
1.333 s
25.998 s
8 mins, 6.008 s
0.041 s
0.010 s
20.054 s
1.272 s
21.880 s
1.429 s
24.657 s
24.016 s
0.706 s
0.664 s
0.774 s
0.457 s
0.842 s
0.771 s
0.852 s
21.172 s
3 mins, 30.043 s
0.040 s
0.008 s
20.155 s
1.400 s
21.771 s
1.020 s
24.229 s
24.542 s
0.515 s
0.783 s
0.930 s
0.917 s
0.793 s
1.234 s
0.880 s
25.362 s
7 mins, 53.805 s
0.034 s
0.009 s
20.772 s
1.691 s
22.098 s
0.675 s
24.828 s
23.657 s
0.792 s
0.745 s
0.777 s
0.757 s
0.637 s
1.013 s
0.992 s
26.418 s
20 mins, 11.922 s
0.038 s
0.008 s
21.034 s
1.495 s
22.403 s
1.433 s
26.868 s
22.792 s
0.779 s
0.285 s
0.917 s
0.760 s
1.374 s
2.180 s
2.093 s
27.829 s
17 mins, 2.833 s
0.031 s
0.008 s
20.644 s
1.336 s
23.132 s
0.774 s
25.159 s
23.351 s
0.658 s
0.590 s
0.448 s
0.966 s
0.463 s
1.339 s
1.353 s
25.883 s
8 mins, 6.532 s
0.038 s
0.011 s
20.404 s
1.292 s
22.309 s
1.664 s
25.808 s
22.485 s
0.925 s
0.557 s
0.555 s
0.778 s
1.190 s
1.008 s
1.348 s
25.264 s
9 mins, 34.480 s
0.052 s
0.011 s
14.466 s
0.088 s
23.916 s
1.932 s
24.005 s
25.392 s
2.125 s
1.050 s
1.453 s
0.814 s
1.286 s
0.992 s
1.229 s
23.399 s
4 mins, 51.087 s
0.048 s
0.008 s
20.872 s
1.438 s
20.512 s
1.053 s
21.987 s
25.339 s
2.079 s
0.950 s
0.704 s
0.808 s
1.328 s
0.958 s
1.154 s
25.176 s
11 mins, 9.081 s
0.032 s
0.007 s
21.695 s
1.672 s
22.134 s
1.977 s
25.859 s
21.484 s
0.822 s
0.315 s
0.538 s
0.362 s
1.489 s
1.077 s
2.072 s
26.424 s
10 mins, 22.114 s
0.034 s
0.008 s
20.154 s
0.982 s
22.494 s
1.441 s
25.196 s
23.884 s
0.905 s
0.823 s
0.727 s
0.843 s
1.155 s
1.090 s
2.232 s
26.830 s
12 mins, 24.365 s
0.043 s
0.008 s
20.088 s
1.187 s
22.819 s
0.900 s
25.570 s
23.802 s
0.501 s
0.898 s
0.795 s
0.729 s
1.438 s
0.943 s
2.406 s
28.330 s
20 mins, 6.372 s
0.037 s
0.009 s
20.493 s
1.023 s
21.685 s
1.611 s
25.459 s
23.657 s
0.805 s
0.195 s
0.702 s
1.138 s
1.057 s
1.084 s
1.391 s
26.783 s
15 mins, 29.113 s
0.059 s
0.014 s
21.018 s
1.214 s
22.350 s
1.375 s
26.626 s
22.618 s
0.780 s
0.579 s
0.495 s
0.890 s
1.187 s
1.106 s
2.539 s
25.100 s
15 mins, 33.275 s
0.032 s
0.008 s
20.524 s
1.034 s
22.341 s
0.543 s
24.374 s
24.450 s
0.935 s
0.249 s
0.383 s
0.724 s
1.247 s
1.305 s
0.925 s
24.053 s
4 mins, 23.317 s
0.034 s
0.008 s
20.319 s
0.991 s
22.431 s
0.746 s
24.154 s
23.147 s
0.588 s
1.137 s
0.782 s
0.700 s
0.646 s
0.918 s
0.882 s
19.863 s
1 mins, 27.623 s
0.032 s
0.007 s
20.935 s
0.868 s
23.092 s
1.484 s
26.594 s
22.025 s
0.672 s
0.649 s
0.768 s
0.689 s
0.969 s
0.494 s
1.554 s
25.856 s
10 mins, 7.862 s
0.036 s
0.009 s
14.985 s
0.088 s
23.395 s
1.666 s
23.871 s
25.660 s
1.557 s
2.363 s
0.717 s
0.804 s
1.280 s
0.808 s
0.983 s
20.591 s
5 mins, 35.860 s
0.057 s
0.014 s
19.610 s
0.990 s
21.766 s
1.220 s
25.283 s
24.481 s
0.666 s
0.655 s
0.579 s
0.399 s
1.005 s
1.054 s
1.017 s
24.528 s
20 mins, 14.596 s
0.032 s
0.008 s
21.311 s
2.075 s
20.850 s
1.080 s
24.416 s
23.627 s
0.670 s
0.704 s
0.758 s
0.857 s
0.805 s
1.163 s
0.956 s
23.931 s
7 mins, 29.391 s
0.051 s
0.012 s
14.436 s
0.056 s
20.480 s
3.403 s
22.646 s
26.926 s
2.011 s
1.638 s
1.634 s
1.159 s
1.053 s
1.193 s
0.642 s
21.163 s
2 mins, 18.504 s
0.036 s
0.014 s
21.230 s
1.389 s
22.136 s
0.864 s
23.513 s
24.149 s
0.575 s
0.596 s
0.591 s
0.833 s
1.010 s
0.915 s
1.025 s
22.950 s
8 mins, 4.909 s
0.035 s
0.009 s
14.808 s
0.056 s
23.672 s
0.698 s
22.495 s
26.450 s
1.093 s
2.400 s
1.810 s
0.749 s
0.938 s
0.768 s
1.386 s
17.010 s
2 mins, 8.960 s
0.051 s
0.012 s
20.925 s
0.970 s
22.628 s
1.244 s
23.903 s
24.197 s
0.664 s
0.798 s
0.811 s
0.859 s
1.062 s
0.812 s
0.947 s
26.333 s
10 mins, 16.052 s
0.033 s
0.008 s
20.919 s
1.570 s
21.998 s
1.458 s
27.303 s
22.230 s
0.753 s
0.865 s
1.062 s
0.868 s
1.471 s
2.800 s
2.871 s
26.794 s
21 mins, 12.644 s
0.060 s
0.012 s
20.421 s
0.405 s
22.382 s
1.434 s
25.777 s
23.648 s
0.737 s
0.499 s
0.737 s
0.780 s
1.096 s
1.316 s
1.120 s
26.199 s
16 mins, 4.638 s
0.055 s
0.007 s
21.090 s
1.790 s
23.218 s
2.446 s
26.298 s
21.144 s
0.745 s
0.824 s
0.637 s
0.815 s
2.015 s
3.123 s
2.222 s
26.261 s
21 mins, 30.176 s
0.055 s
0.012 s
19.236 s
1.403 s
21.771 s
1.689 s
24.319 s
23.838 s
0.968 s
0.556 s
0.842 s
0.607 s
1.175 s
0.956 s
1.070 s
24.552 s
8 mins, 32.689 s
0.053 s
0.013 s
20.581 s
1.418 s
22.535 s
1.183 s
25.752 s
23.097 s
0.816 s
0.564 s
0.897 s
1.017 s
1.298 s
0.761 s
1.590 s
25.573 s
13 mins, 46.972 s
0.038 s
0.008 s
14.415 s
0.093 s
23.971 s
0.878 s
22.247 s
25.135 s
1.078 s
1.364 s
1.800 s
2.050 s
1.113 s
1.021 s
1.064 s
2.222 s
1 mins, 38.017 s
0.035 s
0.009 s
20.701 s
1.336 s
22.287 s
1.650 s
25.377 s
22.470 s
0.852 s
0.632 s
0.400 s
0.624 s
1.303 s
1.121 s
1.609 s
27.027 s
16 mins, 35.941 s
0.032 s
0.008 s
20.842 s
1.032 s
24.340 s
2.168 s
24.918 s
21.469 s
0.609 s
0.590 s
0.820 s
0.389 s
1.297 s
1.714 s
2.487 s
26.640 s
12 mins, 20.175 s
0.032 s
0.007 s
20.271 s
0.804 s
21.684 s
1.497 s
25.089 s
24.000 s
0.551 s
0.721 s
0.934 s
0.674 s
1.030 s
1.315 s
1.014 s
26.171 s
9 mins, 39.492 s
0.033 s
0.008 s
21.278 s
2.389 s
21.893 s
2.191 s
24.877 s
22.536 s
0.636 s
0.788 s
0.713 s
0.934 s
0.938 s
1.270 s
2.863 s
27.614 s
19 mins, 47.999 s
0.040 s
0.011 s
20.290 s
1.247 s
22.137 s
1.404 s
25.759 s
22.851 s
0.743 s
0.553 s
0.608 s
0.662 s
0.807 s
0.996 s
0.901 s
26.349 s
17 mins, 3.823 s
0.032 s
0.007 s
19.559 s
1.477 s
21.905 s
1.345 s
22.239 s
24.810 s
1.705 s
0.859 s
0.659 s
0.576 s
0.916 s
0.811 s
0.989 s
23.150 s
3 mins, 35.163 s
0.033 s
0.008 s
20.431 s
1.324 s
23.556 s
1.165 s
24.870 s
23.437 s
0.756 s
0.563 s
0.722 s
0.287 s
1.224 s
1.120 s
2.832 s
26.525 s
14 mins, 50.320 s
0.033 s
0.008 s
20.744 s
1.079 s
22.905 s
1.362 s
25.596 s
22.865 s
0.424 s
0.672 s
0.846 s
0.347 s
1.201 s
0.931 s
1.068 s
26.567 s
20 mins, 12.366 s
0.033 s
0.007 s
20.439 s
1.469 s
22.769 s
1.307 s
24.594 s
23.434 s
0.827 s
0.553 s
0.782 s
0.724 s
1.310 s
0.968 s
1.937 s
26.176 s
16 mins, 54.664 s
0.032 s
0.007 s
19.962 s
1.208 s
21.546 s
1.533 s
24.061 s
25.019 s
0.846 s
0.840 s
0.716 s
0.819 s
0.424 s
0.889 s
0.956 s
26.961 s
13 mins, 8.897 s
0.037 s
0.008 s
20.462 s
0.676 s
23.355 s
1.023 s
25.204 s
23.397 s
0.792 s
0.755 s
0.706 s
0.531 s
1.351 s
0.736 s
0.911 s
24.697 s
12 mins, 12.419 s
0.033 s
0.008 s
20.079 s
0.911 s
21.154 s
1.430 s
24.817 s
24.065 s
1.448 s
0.686 s
0.626 s
0.821 s
0.827 s
0.453 s
1.144 s
23.660 s
9 mins, 10.582 s
0.033 s
0.008 s
20.339 s
0.776 s
22.850 s
1.595 s
26.684 s
22.516 s
0.437 s
0.349 s
0.915 s
0.921 s
1.230 s
1.137 s
2.044 s
26.200 s
14 mins, 46.529 s
0.032 s
0.008 s
20.689 s
1.178 s
21.024 s
1.376 s
25.157 s
24.237 s
0.683 s
0.723 s
0.674 s
0.820 s
1.160 s
1.007 s
0.852 s
27.143 s
4 mins, 26.942 s
0.051 s
0.008 s
20.260 s
0.797 s
21.558 s
1.472 s
22.106 s
25.535 s
1.434 s
0.757 s
0.543 s
0.792 s
1.257 s
0.323 s
0.578 s
23.805 s
5 mins, 30.850 s
0.032 s
0.008 s
20.606 s
1.202 s
22.429 s
1.136 s
25.894 s
23.131 s
0.738 s
0.970 s
0.752 s
0.922 s
0.926 s
0.894 s
1.935 s
28.818 s
14 mins, 4.233 s
0.031 s
0.008 s
20.555 s
0.980 s
22.721 s
2.292 s
24.465 s
23.315 s
0.715 s
0.469 s
0.750 s
0.943 s
1.394 s
1.548 s
3.762 s
27.846 s
16 mins, 38.404 s
0.035 s
0.021 s
20.568 s
0.993 s
22.645 s
1.089 s
24.181 s
24.070 s
0.694 s
0.849 s
0.594 s
0.748 s
0.705 s
0.987 s
0.629 s
25.081 s
4 mins, 52.997 s
0.031 s
0.007 s
20.775 s
1.439 s
21.009 s
2.059 s
25.494 s
23.710 s
0.795 s
0.779 s
0.927 s
0.869 s
0.964 s
0.990 s
2.496 s
27.600 s
18 mins, 46.646 s
0.033 s
0.007 s
20.749 s
1.334 s
23.390 s
2.308 s
25.657 s
22.553 s
0.603 s
0.797 s
0.787 s
0.681 s
1.783 s
2.793 s
2.804 s
26.266 s
20 mins, 52.600 s
0.054 s
0.012 s
19.969 s
1.201 s
22.602 s
1.402 s
25.773 s
23.024 s
0.746 s
0.418 s
0.759 s
1.004 s
0.938 s
1.132 s
1.297 s
26.317 s
12 mins, 16.729 s
0.040 s
0.010 s
14.434 s
0.089 s
23.954 s
0.087 s
21.948 s
24.184 s
0.055 s
0.888 s
1.438 s
1.357 s
3.322 s
1.865 s
1.067 s
4.031 s
2 mins, 19.596 s
0.033 s
0.008 s
19.582 s
1.241 s
21.849 s
1.473 s
24.986 s
24.414 s
0.634 s
0.876 s
0.630 s
0.751 s
0.787 s
1.149 s
1.320 s
25.247 s
6 mins, 46.347 s
0.052 s
0.009 s
13.268 s
1.130 s
23.981 s
1.450 s
23.267 s
25.943 s
2.715 s
1.539 s
1.128 s
0.790 s
0.975 s
1.125 s
1.377 s
22.804 s
4 mins, 13.332 s
0.032 s
0.007 s
21.152 s
1.911 s
22.406 s
1.567 s
25.641 s
22.392 s
0.838 s
0.906 s
0.807 s
0.861 s
1.024 s
1.128 s
2.370 s
26.945 s
16 mins, 20.167 s
0.033 s
0.008 s
20.046 s
0.940 s
21.321 s
1.886 s
25.019 s
24.262 s
0.704 s
0.852 s
0.666 s
0.780 s
1.000 s
1.022 s
0.881 s
24.184 s
7 mins, 10.963 s
0.039 s
0.008 s
21.185 s
1.916 s
22.774 s
2.282 s
24.794 s
22.207 s
0.675 s
0.939 s
0.711 s
0.910 s
1.140 s
2.083 s
3.474 s
27.084 s
22 mins, 32.710 s
0.054 s
0.013 s
15.815 s
1.719 s
20.858 s
0.081 s
23.096 s
26.471 s
2.170 s
2.103 s
1.402 s
0.797 s
1.136 s
1.148 s
0.492 s
20.713 s
2 mins, 57.769 s
0.053 s
0.012 s
20.294 s
0.972 s
22.652 s
0.896 s
24.547 s
24.329 s
0.776 s
0.677 s
0.678 s
0.957 s
0.708 s
0.897 s
0.393 s
24.427 s
7 mins, 28.523 s
0.035 s
0.009 s
21.024 s
1.175 s
22.235 s
1.946 s
26.708 s
21.521 s
0.730 s
0.714 s
0.697 s
0.891 s
1.252 s
1.277 s
2.036 s
26.605 s
16 mins, 55.319 s
0.060 s
0.011 s
20.910 s
1.129 s
23.171 s
1.278 s
26.666 s
22.151 s
0.702 s
0.854 s
0.716 s
1.020 s
0.886 s
1.187 s
2.357 s
28.826 s
18 mins, 47.297 s
0.035 s
0.009 s
20.574 s
1.142 s
22.880 s
1.073 s
25.358 s
22.990 s
0.755 s
0.514 s
0.829 s
0.660 s
1.104 s
1.090 s
1.490 s
27.032 s
15 mins, 57.422 s
0.034 s
0.008 s
20.913 s
1.190 s
21.744 s
0.877 s
20.917 s
25.992 s
1.312 s
0.537 s
0.735 s
0.860 s
1.159 s
0.506 s
0.545 s
20.065 s
44.211 s
0.096 s
0.019 s
20.774 s
1.438 s
21.613 s
0.987 s
25.335 s
23.668 s
0.763 s
0.758 s
0.596 s
0.715 s
1.504 s
1.041 s
1.544 s
25.184 s
11 mins, 12.750 s
0.067 s
0.013 s
20.425 s
1.228 s
23.089 s
1.763 s
25.785 s
22.205 s
0.873 s
0.689 s
0.582 s
0.405 s
1.067 s
1.333 s
2.473 s
25.485 s
10 mins, 28.956 s
0.050 s
0.008 s
21.102 s
1.049 s
23.264 s
2.162 s
26.584 s
21.575 s
0.562 s
0.831 s
0.420 s
0.819 s
0.743 s
1.034 s
2.698 s
28.038 s
19 mins, 3.698 s
0.042 s
0.008 s
19.637 s
1.552 s
21.756 s
1.586 s
23.927 s
24.621 s
0.398 s
0.754 s
0.746 s
0.719 s
0.835 s
0.813 s
0.911 s
23.091 s
2 mins, 19.092 s
0.032 s
0.008 s
20.425 s
0.985 s
20.956 s
1.754 s
25.530 s
24.226 s
0.625 s
0.768 s
0.754 s
0.919 s
1.070 s
1.117 s
1.387 s
27.003 s
9 mins, 29.463 s
0.035 s
0.008 s
20.984 s
0.875 s
21.811 s
1.388 s
26.480 s
22.525 s
0.697 s
0.607 s
0.771 s
0.558 s
0.937 s
1.078 s
0.835 s
25.535 s
7 mins, 24.871 s
0.047 s
0.010 s
20.613 s
1.145 s
23.603 s
0.977 s
25.341 s
22.830 s
0.650 s
0.938 s
0.854 s
0.928 s
0.958 s
1.317 s
2.442 s
25.720 s
18 mins, 42.974 s
0.032 s
0.008 s
20.251 s
1.112 s
22.251 s
1.258 s
24.498 s
24.108 s
0.613 s
0.542 s
0.681 s
0.682 s
0.923 s
0.996 s
1.113 s
25.905 s
14 mins, 45.194 s
0.032 s
0.008 s
20.680 s
0.927 s
22.709 s
0.816 s
24.100 s
23.337 s
1.213 s
0.876 s
0.866 s
0.693 s
1.072 s
1.330 s
0.857 s
26.951 s
13 mins, 39.630 s
0.052 s
0.012 s
14.407 s
0.091 s
20.064 s
0.483 s
28.012 s
23.014 s
1.143 s
1.441 s
1.618 s
1.802 s
2.275 s
1.183 s
0.885 s
3.095 s
2 mins, 54.499 s
0.034 s
0.009 s
14.570 s
0.097 s
23.942 s
0.080 s
23.042 s
25.498 s
1.134 s
1.145 s
1.067 s
1.836 s
1.352 s
0.983 s
0.986 s
3.000 s
2 mins, 40.182 s
0.055 s
0.013 s
20.325 s
0.958 s
22.845 s
1.369 s
25.833 s
23.147 s
0.737 s
0.287 s
1.025 s
0.339 s
1.153 s
1.195 s
2.417 s
27.323 s
11 mins, 31.198 s
0.044 s
0.009 s
20.959 s
0.906 s
22.018 s
1.321 s
22.652 s
25.513 s
0.812 s
0.742 s
0.660 s
0.904 s
0.624 s
0.574 s
1.078 s
23.662 s
3 mins, 35.986 s
0.034 s
0.009 s
21.370 s
2.732 s
21.780 s
2.304 s
25.300 s
22.511 s
0.530 s
0.623 s
0.727 s
0.888 s
0.963 s
1.101 s
2.208 s
26.766 s
10 mins, 41.460 s
0.032 s
0.007 s
20.726 s
1.137 s
22.101 s
1.517 s
24.964 s
23.952 s
0.884 s
0.653 s
0.940 s
0.412 s
1.391 s
0.984 s
1.191 s
25.772 s
9 mins, 46.219 s
0.042 s
0.007 s
20.382 s
1.077 s
23.112 s
1.392 s
24.885 s
23.487 s
0.691 s
0.749 s
0.932 s
0.863 s
1.030 s
0.626 s
2.183 s
26.528 s
8 mins, 28.368 s
0.035 s
0.008 s
21.077 s
1.321 s
23.289 s
2.212 s
25.398 s
22.356 s
0.833 s
0.679 s
0.810 s
0.660 s
0.627 s
2.460 s
3.424 s
26.711 s
18 mins, 52.854 s
0.036 s
0.008 s
20.829 s
0.827 s
21.367 s
1.225 s
24.864 s
24.312 s
0.834 s
0.752 s
0.679 s
0.774 s
0.940 s
1.287 s
0.941 s
24.134 s
3 mins, 41.294 s
0.032 s
0.008 s
20.615 s
1.348 s
22.437 s
0.581 s
24.992 s
24.379 s
0.593 s
0.855 s
0.589 s
0.763 s
1.102 s
1.032 s
2.812 s
26.745 s
18 mins, 19.907 s
0.032 s
0.007 s
19.770 s
1.179 s
22.577 s
1.686 s
25.076 s
23.713 s
0.670 s
0.876 s
0.818 s
0.790 s
1.350 s
0.900 s
1.438 s
26.018 s
9 mins, 45.931 s
0.037 s
0.008 s
20.599 s
1.585 s
23.156 s
1.799 s
26.128 s
22.039 s
0.890 s
0.366 s
1.106 s
0.669 s
0.998 s
1.669 s
1.956 s
25.997 s
13 mins, 30.425 s
0.031 s
0.008 s
20.354 s
1.011 s
22.998 s
1.429 s
23.897 s
24.424 s
0.625 s
0.424 s
0.986 s
0.887 s
1.537 s
1.018 s
1.481 s
27.750 s
17 mins, 11.982 s
0.033 s
0.008 s
20.398 s
1.592 s
22.007 s
0.802 s
25.367 s
23.216 s
0.688 s
0.672 s
0.794 s
0.511 s
0.813 s
1.326 s
1.174 s
26.221 s
11 mins, 20.221 s
0.037 s
0.011 s
20.785 s
1.079 s
22.764 s
0.953 s
26.295 s
22.988 s
0.806 s
0.920 s
0.395 s
0.851 s
1.029 s
0.756 s
1.581 s
26.850 s
15 mins, 25.481 s
0.035 s
0.008 s
15.079 s
0.089 s
19.982 s
3.329 s
21.826 s
24.650 s
0.096 s
0.936 s
1.475 s
2.054 s
2.955 s
1.939 s
1.179 s
3.387 s
2 mins, 14.909 s
0.034 s
0.008 s
21.275 s
2.652 s
23.525 s
1.505 s
22.689 s
22.420 s
0.688 s
0.653 s
0.819 s
0.686 s
1.633 s
1.001 s
1.750 s
27.920 s
11 mins, 26.365 s
0.035 s
0.007 s
20.296 s
0.754 s
22.267 s
0.869 s
26.356 s
24.456 s
0.715 s
0.468 s
0.541 s
1.062 s
1.133 s
0.784 s
3.017 s
27.610 s
19 mins, 23.608 s
0.033 s
0.008 s
21.210 s
2.547 s
21.990 s
1.924 s
24.533 s
23.442 s
0.613 s
0.773 s
0.626 s
0.934 s
1.240 s
1.931 s
3.736 s
26.867 s
20 mins, 25.894 s
0.067 s
0.014 s
20.974 s
1.203 s
22.470 s
0.802 s
26.253 s
23.275 s
0.700 s
0.691 s
0.818 s
0.666 s
1.446 s
1.713 s
1.547 s
29.730 s
19 mins, 53.439 s
0.054 s
0.011 s
20.360 s
0.821 s
22.216 s
1.169 s
22.010 s
24.781 s
2.271 s
0.601 s
0.764 s
0.771 s
0.994 s
1.006 s
1.064 s
25.122 s
7 mins, 40.791 s
0.035 s
0.009 s
15.378 s
2.858 s
21.523 s
0.781 s
22.681 s
26.385 s
1.559 s
2.043 s
0.804 s
0.747 s
1.262 s
1.364 s
0.977 s
20.262 s
3 mins, 21.045 s
0.033 s
0.007 s
20.321 s
1.019 s
23.331 s
1.534 s
25.514 s
23.307 s
0.832 s
0.751 s
0.684 s
0.966 s
1.056 s
1.878 s
2.260 s
28.684 s
21 mins, 9.438 s
0.051 s
0.011 s
20.152 s
0.917 s
22.294 s
1.176 s
25.116 s
23.552 s
0.519 s
0.605 s
0.581 s
0.780 s
1.210 s
1.516 s
0.940 s
25.700 s
10 mins, 30.506 s
0.033 s
0.008 s
19.780 s
0.980 s
21.599 s
1.440 s
22.130 s
23.530 s
1.420 s
0.974 s
1.086 s
0.729 s
1.079 s
1.379 s
1.241 s
21.622 s
5 mins, 13.936 s
0.034 s
0.009 s
20.668 s
1.166 s
22.122 s
0.974 s
24.522 s
24.267 s
0.505 s
0.469 s
0.718 s
0.330 s
0.936 s
0.890 s
1.063 s
25.579 s
3 mins, 46.090 s
0.036 s
0.008 s
20.503 s
1.085 s
22.868 s
1.440 s
27.753 s
22.030 s
0.736 s
0.628 s
0.401 s
1.034 s
0.999 s
2.118 s
2.117 s
25.652 s
16 mins, 13.741 s
0.031 s
0.008 s
20.025 s
1.138 s
21.569 s
1.255 s
22.066 s
26.871 s
0.848 s
0.697 s
0.700 s
0.570 s
0.860 s
1.046 s
1.034 s
24.648 s
5 mins, 37.407 s
0.035 s
0.007 s
21.149 s
1.854 s
23.977 s
1.728 s
25.439 s
22.361 s
0.364 s
0.331 s
1.024 s
0.865 s
1.292 s
2.522 s
3.216 s
26.130 s
21 mins, 9.241 s
0.039 s
0.010 s
20.686 s
1.110 s
23.445 s
2.154 s
22.965 s
23.295 s
0.942 s
0.541 s
0.802 s
0.763 s
0.523 s
1.173 s
1.027 s
26.049 s
7 mins, 38.922 s
0.057 s
0.013 s
21.171 s
0.717 s
22.589 s
1.107 s
24.688 s
23.991 s
0.484 s
0.825 s
0.582 s
0.779 s
0.802 s
1.075 s
0.905 s
27.491 s
11 mins, 49.570 s
0.043 s
0.009 s
20.905 s
1.163 s
22.890 s
1.055 s
24.247 s
23.147 s
0.817 s
0.638 s
0.732 s
0.696 s
1.077 s
0.922 s
1.307 s
27.546 s
15 mins, 27.662 s
0.036 s
0.012 s
20.428 s
1.197 s
24.074 s
2.952 s
26.606 s
19.689 s
0.762 s
0.644 s
0.428 s
0.814 s
1.154 s
1.228 s
2.861 s
27.549 s
22 mins, 20.108 s
0.033 s
0.008 s
20.802 s
1.720 s
22.386 s
1.480 s
26.082 s
23.254 s
0.677 s
0.666 s
0.323 s
0.888 s
0.980 s
1.483 s
2.252 s
27.607 s
14 mins, 18.877 s
0.037 s
0.009 s
21.208 s
2.098 s
22.108 s
2.358 s
27.450 s
19.491 s
0.808 s
0.221 s
0.838 s
1.051 s
1.322 s
1.285 s
1.564 s
25.795 s
17 mins, 57.118 s
0.046 s
0.012 s
20.721 s
1.268 s
22.684 s
1.100 s
25.725 s
23.520 s
0.697 s
1.028 s
0.345 s
1.067 s
0.907 s
1.190 s
1.491 s
25.938 s
14 mins, 16.294 s
0.031 s
0.007 s
20.635 s
1.030 s
22.231 s
0.966 s
24.048 s
24.557 s
0.576 s
0.864 s
0.763 s
0.995 s
1.273 s
0.906 s
1.359 s
25.836 s
7 mins, 17.760 s
0.034 s
0.012 s
21.158 s
2.752 s
22.718 s
2.127 s
26.633 s
20.929 s
0.572 s
0.253 s
1.000 s
0.661 s
1.158 s
2.126 s
3.135 s
25.971 s
19 mins, 47.820 s
0.041 s
0.010 s
19.628 s
1.459 s
22.781 s
1.219 s
24.966 s
23.035 s
0.874 s
0.719 s
0.722 s
0.468 s
1.028 s
0.910 s
0.836 s
23.912 s
4 mins, 59.726 s
0.033 s
0.009 s
20.292 s
0.866 s
21.658 s
1.118 s
24.360 s
24.708 s
0.662 s
0.680 s
0.630 s
0.783 s
0.910 s
0.855 s
0.906 s
25.302 s
4 mins, 46.653 s
0.034 s
0.008 s
20.785 s
0.731 s
22.522 s
1.535 s
22.845 s
25.187 s
0.612 s
0.553 s
0.680 s
1.061 s
0.689 s
1.049 s
0.757 s
24.853 s
11 mins, 23.969 s
0.034 s
0.008 s
20.389 s
1.277 s
22.726 s
0.721 s
25.236 s
23.205 s
0.525 s
0.759 s
0.882 s
0.629 s
0.909 s
1.002 s
0.823 s
26.563 s
8 mins, 6.247 s
0.038 s
0.012 s
20.623 s
1.494 s
22.451 s
1.356 s
23.868 s
24.719 s
0.446 s
0.600 s
0.648 s
0.858 s
0.890 s
1.022 s
0.783 s
27.316 s
13 mins, 7.799 s
0.035 s
0.008 s
21.155 s
0.835 s
22.927 s
1.475 s
24.317 s
23.404 s
0.644 s
0.709 s
0.712 s
0.579 s
0.767 s
0.882 s
0.826 s
25.458 s
10 mins, 5.721 s
0.034 s
0.008 s
20.885 s
1.791 s
21.874 s
1.894 s
25.692 s
22.450 s
0.660 s
0.296 s
0.902 s
0.875 s
1.325 s
1.094 s
2.809 s
27.137 s
18 mins, 49.483 s
0.047 s
0.008 s
20.229 s
1.258 s
22.752 s
1.443 s
25.427 s
22.984 s
0.778 s
0.688 s
0.993 s
0.722 s
1.489 s
1.352 s
2.356 s
27.446 s
17 mins, 15.681 s
0.035 s
0.011 s
20.857 s
0.825 s
22.734 s
1.408 s
27.886 s
22.297 s
0.758 s
0.658 s
0.853 s
0.736 s
0.881 s
2.143 s
3.306 s
26.521 s
15 mins, 32.290 s
0.033 s
0.007 s
20.552 s
1.147 s
22.899 s
2.377 s
23.153 s
23.978 s
0.788 s
0.679 s
0.822 s
0.386 s
1.219 s
0.996 s
1.499 s
24.659 s
6 mins, 45.950 s
0.035 s
0.011 s
20.060 s
0.980 s
22.847 s
0.950 s
24.928 s
24.484 s
0.710 s
0.637 s
0.784 s
0.787 s
1.387 s
1.028 s
1.483 s
25.368 s
8 mins, 25.224 s
0.033 s
0.008 s
20.792 s
0.838 s
22.694 s
0.563 s
25.130 s
24.094 s
0.766 s
0.854 s
0.721 s
0.729 s
1.322 s
0.926 s
1.464 s
27.585 s
17 mins, 56.379 s
0.036 s
0.010 s
19.941 s
1.123 s
23.109 s
1.960 s
28.014 s
21.156 s
0.973 s
0.468 s
0.606 s
0.829 s
0.892 s
1.910 s
2.220 s
27.394 s
14 mins, 45.902 s
0.036 s
0.007 s
20.569 s
1.220 s
23.270 s
1.392 s
23.919 s
23.687 s
0.661 s
0.318 s
0.794 s
0.713 s
0.478 s
0.999 s
1.260 s
26.631 s
5 mins, 15.232 s
0.069 s
0.009 s
20.477 s
1.148 s
22.665 s
0.711 s
25.623 s
23.270 s
0.758 s
0.738 s
0.916 s
0.398 s
0.991 s
0.912 s
0.533 s
26.614 s
12 mins, 24.350 s
0.040 s
0.009 s
20.917 s
1.119 s
22.898 s
1.323 s
24.755 s
24.055 s
0.818 s
0.352 s
0.742 s
0.921 s
1.027 s
1.027 s
1.673 s
27.851 s
15 mins, 24.244 s
0.034 s
0.010 s
19.991 s
1.299 s
22.693 s
1.449 s
26.171 s
23.237 s
0.651 s
0.689 s
0.579 s
1.096 s
1.050 s
0.987 s
1.293 s
26.100 s
9 mins, 25.595 s
0.033 s
0.012 s
20.623 s
1.216 s
23.026 s
1.481 s
24.041 s
23.533 s
0.873 s
0.657 s
0.685 s
0.870 s
0.842 s
0.896 s
1.273 s
25.876 s
13 mins, 30.869 s
0.033 s
0.007 s
0.070 s
0.005 s
0.004 s
5 mins, 37.667 s
2 mins, 50.630 s
2 mins, 1.442 s
2 mins, 1.597 s
36.010 s
20.183 s
4.831 s
3 mins, 33.700 s
1 mins, 27.378 s

Pipeline Stages


    Branch 1

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUB001.bam
    Commands
    Outputs
    • data/ubam/PNG_XUB001.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:49 (16.007 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUB001.reverted.bam
    • data/ubam/PNG_XUB001.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUB001.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:49 - 2016-5-16 11:15:52 (2.911 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUB001.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUB001.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:52 - 2016-5-16 11:16:13 (21.131 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUB001.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:13 (0.841 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:14 - 2016-5-16 11:16:37 (23.009 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:37 - 2016-5-16 11:16:59 (22.287 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:16:59 - 2016-5-16 11:17:1 (1.301 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:1 - 2016-5-16 11:17:3 (1.811 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:3 - 2016-5-16 11:17:4 (1.109 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:4 - 2016-5-16 11:17:5 (1.087 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (2.174 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:7 (0.989 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:8 (0.889 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:13 (3.651 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21335
    Outputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:19:44 (2 minutes, 31.072 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21502
    Outputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:19:44 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:19:44 (0.008 seconds)

    Branch 2

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUC021.bam
    Commands
    Outputs
    • data/ubam/PNG_XUC021.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.274 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUC021.reverted.bam
    • data/ubam/PNG_XUC021.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUC021.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.125 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUC021.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUC021.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.963 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUC021.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.419 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:44 (25.610 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.637 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.838 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.807 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.965 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.745 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.252 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.156 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.621 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.807 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21456
    Outputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:35:39 (17 minutes, 55.226 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21854
    Outputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:35:39 (0.043 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:35:39 (0.012 seconds)

    Branch 3

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUA012.bam
    Commands
    Outputs
    • data/ubam/PNG_XUA012.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.284 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUA012.reverted.bam
    • data/ubam/PNG_XUA012.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUA012.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.798 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUA012.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUA012.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.106 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUA012.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:17 (1.318 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:40 (22.794 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:40 - 2016-5-16 11:17:7 (26.739 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.644 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.740 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.717 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.730 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.800 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.308 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.029 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:35 (22.311 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21346
    Outputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:35 - 2016-5-16 11:21:25 (3 minutes, 50.415 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21544
    Outputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:21:25 (0.053 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:21:25 (0.008 seconds)

    Branch 4

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUA011.bam
    Commands
    Outputs
    • data/ubam/PNG_XUA011.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.903 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUA011.reverted.bam
    • data/ubam/PNG_XUA011.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUA011.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.890 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUA011.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUA011.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.570 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUA011.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.972 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.277 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.294 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.745 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.658 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.675 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.775 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.437 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.986 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.919 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.174 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21357
    Outputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:23:13 (5 minutes, 34.706 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21580
    Outputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:23:13 (0.052 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:23:13 (0.013 seconds)

    Branch 5

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XPA028.bam
    Commands
    Outputs
    • data/ubam/PNG_XPA028.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.946 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XPA028.reverted.bam
    • data/ubam/PNG_XPA028.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XPA028.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.279 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XPA028.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XPA028.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.714 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XPA028.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.584 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.368 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.851 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.685 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.709 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.731 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.729 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.471 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.821 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.083 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:37 (23.669 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21367
    Outputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:37 - 2016-5-16 11:26:2 (8 minutes, 25.317 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21634
    Outputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:26:2 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:26:2 (0.009 seconds)

    Branch 6

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUC022.bam
    Commands
    Outputs
    • data/ubam/PNG_XUC022.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.752 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUC022.reverted.bam
    • data/ubam/PNG_XUC022.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUC022.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.203 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUC022.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUC022.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.884 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUC022.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.299 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.114 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.000 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.725 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.924 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.849 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.752 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.136 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.249 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.883 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:44 (28.291 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21444
    Outputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:34:20 (16 minutes, 35.496 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21826
    Outputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:34:20 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:34:20 (0.007 seconds)

    Branch 7

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_DRS015A.bam
    Commands
    Outputs
    • data/ubam/PNG_DRS015A.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.731 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_DRS015A.reverted.bam
    • data/ubam/PNG_DRS015A.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_DRS015A.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.773 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_DRS015A.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_DRS015A.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.627 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_DRS015A.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.298 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.831 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.487 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.691 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.725 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.710 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.028 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.121 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.955 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.115 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (25.812 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21413
    Outputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:30:7 (12 minutes, 27.021 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21730
    Outputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:30:7 (0.036 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:30:7 (0.008 seconds)

    Branch 8

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUA001.bam
    Commands
    Outputs
    • data/ubam/PNG_XUA001.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.253 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUA001.reverted.bam
    • data/ubam/PNG_XUA001.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUA001.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.177 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUA001.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUA001.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.602 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUA001.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.971 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.710 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.289 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.748 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.696 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.935 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.027 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.114 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.442 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.035 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:46 (29.399 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21462
    Outputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:36:48 (19 minutes, 2.280 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21881
    Outputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:36:48 (0.037 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:36:49 (0.009 seconds)

    Branch 9

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XIA508.bam
    Commands
    Outputs
    • data/ubam/PNG_XIA508.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.333 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XIA508.reverted.bam
    • data/ubam/PNG_XIA508.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XIA508.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.634 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XIA508.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XIA508.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.016 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XIA508.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.215 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:44 (23.476 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.241 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.871 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.769 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.629 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.737 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.153 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.186 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.022 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (26.432 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21388
    Outputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:27:33 (9 minutes, 52.736 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21670
    Outputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:33 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:33 (0.008 seconds)

    Branch 10

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_DRS034.bam
    Commands
    Outputs
    • data/ubam/PNG_DRS034.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.769 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_DRS034.reverted.bam
    • data/ubam/PNG_DRS034.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_DRS034.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.034 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_DRS034.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_DRS034.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.426 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_DRS034.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.053 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.714 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.988 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.789 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.664 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.701 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.985 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.458 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.855 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.114 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (27.275 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21461
    Outputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:36:18 (18 minutes, 34.704 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21862
    Outputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:36:18 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:36:18 (0.009 seconds)

    Branch 11

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUA030.bam
    Commands
    Outputs
    • data/ubam/PNG_XUA030.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.577 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUA030.reverted.bam
    • data/ubam/PNG_XUA030.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUA030.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:47 (0.101 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUA030.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUA030.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:6 (18.801 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUA030.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:7 - 2016-5-16 11:16:12 (4.837 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:34 (22.930 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:35 - 2016-5-16 11:17:0 (25.989 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:1 - 2016-5-16 11:17:3 (2.014 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:3 - 2016-5-16 11:17:5 (1.794 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:6 (1.229 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.446 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.209 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.250 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:10 (0.677 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:26 (14.783 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21337
    Outputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:26 - 2016-5-16 11:20:26 (3 minutes, 0.645 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21517
    Outputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:20:26 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:20:26 (0.009 seconds)

    Branch 12

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUC009.bam
    Commands
    Outputs
    • data/ubam/PNG_XUC009.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.663 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUC009.reverted.bam
    • data/ubam/PNG_XUC009.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUC009.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.204 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUC009.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUC009.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (21.862 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUC009.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.504 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (27.131 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.614 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.832 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.731 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.028 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.945 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.239 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.446 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:19 (2.446 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:19 - 2016-5-16 11:17:45 (25.791 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21469
    Outputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:45 - 2016-5-16 11:37:55 (20 minutes, 9.177 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21910
    Outputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:55 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:55 (0.008 seconds)

    Branch 13

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUA020.bam
    Commands
    Outputs
    • data/ubam/PNG_XUA020.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.237 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUA020.reverted.bam
    • data/ubam/PNG_XUA020.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUA020.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.157 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUA020.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUA020.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.543 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUA020.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.310 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.146 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.264 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.757 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.828 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.699 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.845 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.907 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.926 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.089 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (27.209 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21419
    Outputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:31:37 (13 minutes, 55.857 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21766
    Outputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:37 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:37 (0.008 seconds)

    Branch 14

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../BROAD/Madang/PNG_XUC006.bam
    Commands
    Outputs
    • data/ubam/PNG_XUC006.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.601 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PNG_XUC006.reverted.bam
    • data/ubam/PNG_XUC006.reverted.bam
    Commands
    Outputs
    • data/qc/PNG_XUC006.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.824 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PNG_XUC006.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PNG_XUC006.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.611 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PNG_XUC006.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.602 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:41 (23.048 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:41 - 2016-5-16 11:17:6 (24.521 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:6 (0.963 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:7 (0.741 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.959 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.688 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.173 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.979 seconds)
  13. flagstat

    Inputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.155 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:37 (24.410 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21364
    Outputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:37 - 2016-5-16 11:23:51 (6 minutes, 13.767 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21589
    Outputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:23:51 (0.037 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:23:51 (0.010 seconds)

    Branch 15

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0189_C.bam
    Commands
    Outputs
    • data/ubam/PN0189_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.791 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0189_C.reverted.bam
    • data/ubam/PN0189_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0189_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.107 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0189_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0189_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.484 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0189_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.122 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.531 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:6 (22.909 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.457 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:7 (0.714 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.833 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.770 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.821 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.538 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.083 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:35 (22.487 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21351
    Outputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:35 - 2016-5-16 11:21:24 (3 minutes, 48.733 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21538
    Outputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:21:24 (0.038 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:21:24 (0.008 seconds)

    Branch 16

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0160_C.bam
    Commands
    Outputs
    • data/ubam/PN0160_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.585 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0160_C.reverted.bam
    • data/ubam/PN0160_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0160_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 (0.782 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0160_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0160_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:20 (24.768 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0160_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.330 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:22 - 2016-5-16 11:16:46 (23.849 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:8 (21.821 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.794 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.532 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.803 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.870 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.168 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.941 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.657 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (24.641 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21422
    Outputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:31:23 (13 minutes, 42.721 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21760
    Outputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:23 (0.052 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:23 (0.012 seconds)

    Branch 17

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0025_C.bam
    Commands
    Outputs
    • data/ubam/PN0025_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.582 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0025_C.reverted.bam
    • data/ubam/PN0025_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0025_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.945 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0025_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0025_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:19 (23.261 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0025_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.778 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (25.667 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.278 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.743 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.727 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.812 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.623 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.778 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.273 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.605 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (26.728 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21415
    Outputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:30:30 (12 minutes, 46.603 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21736
    Outputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:30:30 (0.031 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:30:30 (0.007 seconds)

    Branch 18

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0127_C.bam
    Commands
    Outputs
    • data/ubam/PN0127_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.245 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0127_C.reverted.bam
    • data/ubam/PN0127_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0127_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.855 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0127_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0127_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.781 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0127_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.835 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (26.828 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.839 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.654 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.549 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.405 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.927 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.006 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.809 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (1.892 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.708 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21427
    Outputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:30:56 (13 minutes, 11.583 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21745
    Outputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:30:56 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:30:56 (0.010 seconds)

    Branch 19

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0182_C.bam
    Commands
    Outputs
    • data/ubam/PN0182_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.375 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0182_C.reverted.bam
    • data/ubam/PN0182_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0182_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.978 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0182_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0182_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.168 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0182_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.186 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.584 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.525 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.886 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.814 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.816 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.082 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.148 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:16 (2.016 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:19 (3.346 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:19 - 2016-5-16 11:17:47 (27.661 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21463
    Outputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:47 - 2016-5-16 11:37:0 (19 minutes, 13.539 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21886
    Outputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:0 (0.031 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:0 (0.007 seconds)

    Branch 20

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0140_C.bam
    Commands
    Outputs
    • data/ubam/PN0140_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.528 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0140_C.reverted.bam
    • data/ubam/PN0140_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0140_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.270 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0140_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0140_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.406 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0140_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.090 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:42 (23.404 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (24.600 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.044 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.599 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.834 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.995 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.990 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.969 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.134 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.124 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21403
    Outputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:28:53 (11 minutes, 12.865 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21699
    Outputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:28:53 (0.064 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:28:53 (0.013 seconds)

    Branch 21

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0042_C.bam
    Commands
    Outputs
    • data/ubam/PN0042_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.436 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0042_C.reverted.bam
    • data/ubam/PN0042_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0042_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.786 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0042_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0042_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.090 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0042_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.711 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (26.300 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.944 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.676 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.709 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.561 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.648 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.111 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.036 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.874 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.241 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21380
    Outputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:26:24 (8 minutes, 43.490 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21646
    Outputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:26:24 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:26:24 (0.009 seconds)

    Branch 22

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0005_C.bam
    Commands
    Outputs
    • data/ubam/PN0005_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.623 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0005_C.reverted.bam
    • data/ubam/PN0005_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0005_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:58 (2.680 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0005_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0005_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:58 - 2016-5-16 11:16:19 (21.079 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0005_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.158 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.114 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.231 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.814 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.769 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.618 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.429 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.269 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.835 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.320 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:43 (27.764 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21429
    Outputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:31:45 (14 minutes, 1.990 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21769
    Outputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:45 (0.052 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:45 (0.013 seconds)

    Branch 23

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0107_C.bam
    Commands
    Outputs
    • data/ubam/PN0107_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.787 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0107_C.reverted.bam
    • data/ubam/PN0107_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0107_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.905 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0107_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0107_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (21.837 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0107_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.100 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.413 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.556 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.576 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.629 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.573 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.980 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.914 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.152 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.873 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.287 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21366
    Outputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:23:19 (5 minutes, 41.153 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21586
    Outputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:23:19 (0.041 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:23:19 (0.008 seconds)

    Branch 24

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0120_C.bam
    Commands
    Outputs
    • data/ubam/PN0120_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.243 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0120_C.reverted.bam
    • data/ubam/PN0120_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0120_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.216 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0120_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0120_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.098 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0120_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.892 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.097 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:8 (24.433 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.795 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.913 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.897 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.362 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.333 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.926 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:16 (2.849 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:41 (25.047 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21431
    Outputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:31:22 (13 minutes, 40.936 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21757
    Outputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:22 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:22 (0.012 seconds)

    Branch 25

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0009_C.bam
    Commands
    Outputs
    • data/ubam/PN0009_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.330 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0009_C.reverted.bam
    • data/ubam/PN0009_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0009_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.518 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0009_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0009_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.160 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0009_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.350 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.356 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (22.919 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.786 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.623 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.669 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.871 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.868 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.261 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.333 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (25.998 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21387
    Outputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:25:46 (8 minutes, 6.008 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21627
    Outputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:46 (0.041 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:46 (0.010 seconds)

    Branch 26

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0022_C.bam
    Commands
    Outputs
    • data/ubam/PN0022_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.054 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0022_C.reverted.bam
    • data/ubam/PN0022_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0022_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.272 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0022_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0022_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.880 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0022_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.429 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.657 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.016 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.706 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.664 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.774 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.457 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.842 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.771 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 (0.852 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:34 (21.172 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21341
    Outputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:34 - 2016-5-16 11:21:4 (3 minutes, 30.043 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21526
    Outputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:21:4 (0.040 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:21:4 (0.008 seconds)

    Branch 27

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0167_C.bam
    Commands
    Outputs
    • data/ubam/PN0167_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.155 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0167_C.reverted.bam
    • data/ubam/PN0167_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0167_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.400 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0167_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0167_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.771 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0167_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.020 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.229 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.542 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.515 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.783 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.930 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.917 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.793 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.234 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.880 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.362 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21377
    Outputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:25:33 (7 minutes, 53.805 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21619
    Outputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:33 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:33 (0.009 seconds)

    Branch 28

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0029_C.bam
    Commands
    Outputs
    • data/ubam/PN0029_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.772 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0029_C.reverted.bam
    • data/ubam/PN0029_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0029_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.691 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0029_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0029_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.098 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0029_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.675 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.828 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.657 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.792 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.745 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.777 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.757 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.637 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.013 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.992 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.418 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21483
    Outputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:37:52 (20 minutes, 11.922 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21906
    Outputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:54 (0.038 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:54 (0.008 seconds)

    Branch 29

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0087_C.bam
    Commands
    Outputs
    • data/ubam/PN0087_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.034 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0087_C.reverted.bam
    • data/ubam/PN0087_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0087_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.495 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0087_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0087_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.403 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0087_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.433 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:47 (26.868 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:10 (22.792 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:10 (0.779 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:11 (0.285 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.917 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.760 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.374 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.180 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:18 (2.093 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:19 - 2016-5-16 11:17:46 (27.829 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21458
    Outputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:34:49 (17 minutes, 2.833 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21841
    Outputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:34:49 (0.031 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:34:49 (0.008 seconds)

    Branch 30

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0185_C.bam
    Commands
    Outputs
    • data/ubam/PN0185_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.644 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0185_C.reverted.bam
    • data/ubam/PN0185_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0185_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.336 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0185_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0185_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.132 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0185_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.774 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.159 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.351 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.658 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.590 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.448 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.966 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.463 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.339 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.353 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (25.883 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21386
    Outputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:25:47 (8 minutes, 6.532 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21631
    Outputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:47 (0.038 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:47 (0.011 seconds)

    Branch 31

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0032_C.bam
    Commands
    Outputs
    • data/ubam/PN0032_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.404 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0032_C.reverted.bam
    • data/ubam/PN0032_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0032_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.292 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0032_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0032_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.309 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0032_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.664 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.808 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.485 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.925 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.557 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.555 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.778 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.190 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.008 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.348 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (25.264 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21374
    Outputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:27:15 (9 minutes, 34.480 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21658
    Outputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:15 (0.052 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:15 (0.011 seconds)

    Branch 32

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0019_C.bam
    Commands
    Outputs
    • data/ubam/PN0019_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.466 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0019_C.reverted.bam
    • data/ubam/PN0019_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0019_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:47 (0.088 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0019_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0019_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.916 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0019_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:13 (1.932 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:13 - 2016-5-16 11:16:37 (24.005 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:38 - 2016-5-16 11:17:3 (25.392 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:3 - 2016-5-16 11:17:5 (2.125 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:6 (1.050 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.453 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.814 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 - 2016-5-16 11:17:10 (1.286 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:10 (0.992 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.229 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:35 (23.399 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21354
    Outputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:36 - 2016-5-16 11:22:27 (4 minutes, 51.087 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21559
    Outputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:22:27 (0.048 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:22:27 (0.008 seconds)

    Branch 33

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0130_C.bam
    Commands
    Outputs
    • data/ubam/PN0130_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.872 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0130_C.reverted.bam
    • data/ubam/PN0130_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0130_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.438 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0130_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0130_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:16 (20.512 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0130_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:17 (1.053 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:39 (21.987 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:39 - 2016-5-16 11:17:5 (25.339 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (2.079 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:7 (0.950 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.704 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.808 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.328 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.958 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.154 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (25.176 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21401
    Outputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:28:47 (11 minutes, 9.081 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21694
    Outputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:28:47 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:28:47 (0.007 seconds)

    Branch 34

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0177_C.bam
    Commands
    Outputs
    • data/ubam/PN0177_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.695 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0177_C.reverted.bam
    • data/ubam/PN0177_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0177_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (1.672 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0177_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0177_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (22.134 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0177_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.977 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:47 (25.859 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (21.484 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.822 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.315 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.538 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.362 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.489 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.077 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.072 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (26.424 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21392
    Outputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:28:5 (10 minutes, 22.114 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21682
    Outputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:28:5 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:28:5 (0.008 seconds)

    Branch 35

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0075_C.bam
    Commands
    Outputs
    • data/ubam/PN0075_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.154 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0075_C.reverted.bam
    • data/ubam/PN0075_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0075_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.982 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0075_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0075_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.494 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0075_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.441 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.196 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.884 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.905 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.823 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.727 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.843 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.155 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.090 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.232 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (26.830 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21421
    Outputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:30:8 (12 minutes, 24.365 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21733
    Outputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:30:8 (0.043 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:30:8 (0.008 seconds)

    Branch 36

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0012_C.bam
    Commands
    Outputs
    • data/ubam/PN0012_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.088 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0012_C.reverted.bam
    • data/ubam/PN0012_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0012_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.187 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0012_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0012_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.819 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0012_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.900 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.570 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.802 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.501 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.898 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.795 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.729 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.438 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.943 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.406 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:45 (28.330 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21466
    Outputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:45 - 2016-5-16 11:37:51 (20 minutes, 6.372 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21901
    Outputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:51 (0.037 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:51 (0.009 seconds)

    Branch 37

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0110_C.bam
    Commands
    Outputs
    • data/ubam/PN0110_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.493 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0110_C.reverted.bam
    • data/ubam/PN0110_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0110_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.023 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0110_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0110_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.685 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0110_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.611 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.459 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.657 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.805 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.195 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.702 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.138 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.057 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.084 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.391 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (26.783 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21440
    Outputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:33:11 (15 minutes, 29.113 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21802
    Outputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:33:11 (0.059 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:33:11 (0.014 seconds)

    Branch 38

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0157_C.bam
    Commands
    Outputs
    • data/ubam/PN0157_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.018 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0157_C.reverted.bam
    • data/ubam/PN0157_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0157_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.214 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0157_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0157_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.350 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0157_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.375 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (26.626 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.618 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.780 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.579 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.495 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.890 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.187 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.106 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.539 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:42 (25.100 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21447
    Outputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:33:15 (15 minutes, 33.275 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21805
    Outputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:33:15 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:33:15 (0.008 seconds)

    Branch 39

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0055_C.bam
    Commands
    Outputs
    • data/ubam/PN0055_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.524 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0055_C.reverted.bam
    • data/ubam/PN0055_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0055_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.034 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0055_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0055_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.341 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0055_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.543 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.374 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (24.450 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.935 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.249 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.383 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.724 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.247 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.305 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 (0.925 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:37 (24.053 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21358
    Outputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:37 - 2016-5-16 11:22:1 (4 minutes, 23.317 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21550
    Outputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:22:1 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:22:1 (0.008 seconds)

    Branch 40

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0097_C.bam
    Commands
    Outputs
    • data/ubam/PN0097_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.319 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0097_C.reverted.bam
    • data/ubam/PN0097_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0097_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.991 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0097_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0097_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.431 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0097_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.746 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.154 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:6 (23.147 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:6 (0.588 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.137 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.782 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.700 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.646 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:10 (0.918 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 (0.882 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:32 (19.863 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21338
    Outputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:32 - 2016-5-16 11:18:59 (1 minutes, 27.623 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21490
    Outputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:18:59 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:18:59 (0.007 seconds)

    Branch 41

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0055_Cx.bam
    Commands
    Outputs
    • data/ubam/PN0055_Cx.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.935 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0055_Cx.reverted.bam
    • data/ubam/PN0055_Cx.reverted.bam
    Commands
    Outputs
    • data/qc/PN0055_Cx.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.868 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0055_Cx.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0055_Cx.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.092 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0055_Cx.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.484 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:47 (26.594 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.025 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.672 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.649 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.768 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.689 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.969 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.494 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.554 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (25.856 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21397
    Outputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:27:49 (10 minutes, 7.862 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21676
    Outputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:49 (0.036 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:49 (0.009 seconds)

    Branch 42

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0059_C.bam
    Commands
    Outputs
    • data/ubam/PN0059_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (14.985 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0059_C.reverted.bam
    • data/ubam/PN0059_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0059_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:48 (0.088 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0059_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0059_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.395 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0059_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:13 (1.666 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:13 - 2016-5-16 11:16:37 (23.871 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:37 - 2016-5-16 11:17:3 (25.660 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:3 - 2016-5-16 11:17:4 (1.557 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (2.363 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:7 (0.717 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.804 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.280 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:10 (0.808 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 (0.983 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:32 (20.591 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21350
    Outputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:32 - 2016-5-16 11:23:8 (5 minutes, 35.860 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21577
    Outputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:23:8 (0.057 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:23:8 (0.014 seconds)

    Branch 43

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0170_C.bam
    Commands
    Outputs
    • data/ubam/PN0170_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.610 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0170_C.reverted.bam
    • data/ubam/PN0170_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0170_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.990 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0170_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0170_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.766 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0170_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.220 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.283 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.481 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.666 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.655 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.579 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.399 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.005 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.054 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.017 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.528 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21484
    Outputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:37:53 (20 minutes, 14.596 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21909
    Outputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:55 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:55 (0.008 seconds)

    Branch 44

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0035_C.bam
    Commands
    Outputs
    • data/ubam/PN0035_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.311 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0035_C.reverted.bam
    • data/ubam/PN0035_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0035_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.075 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0035_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0035_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:18 (20.850 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0035_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.080 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.416 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.627 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.670 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.704 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.758 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.857 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.805 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.163 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.956 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (23.931 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21378
    Outputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:25:7 (7 minutes, 29.391 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21610
    Outputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:7 (0.051 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:7 (0.012 seconds)

    Branch 45

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0090_C.bam
    Commands
    Outputs
    • data/ubam/PN0090_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (14.436 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0090_C.reverted.bam
    • data/ubam/PN0090_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0090_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:48 (0.056 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0090_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0090_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:8 (20.480 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0090_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:8 - 2016-5-16 11:16:12 (3.403 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:34 (22.646 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:34 - 2016-5-16 11:17:1 (26.926 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:1 - 2016-5-16 11:17:3 (2.011 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:3 - 2016-5-16 11:17:5 (1.638 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.634 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.159 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.053 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.193 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:10 (0.642 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:33 (21.163 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21343
    Outputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:33 - 2016-5-16 11:19:51 (2 minutes, 18.504 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21505
    Outputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:19:51 (0.036 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:19:51 (0.014 seconds)

    Branch 46

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0079_C.bam
    Commands
    Outputs
    • data/ubam/PN0079_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.230 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0079_C.reverted.bam
    • data/ubam/PN0079_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0079_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.389 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0079_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0079_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.136 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0079_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.864 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (23.513 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.149 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.575 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.596 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.591 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.833 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.010 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.915 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.025 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:36 (22.950 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21383
    Outputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:36 - 2016-5-16 11:25:41 (8 minutes, 4.909 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21622
    Outputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:41 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:41 (0.009 seconds)

    Branch 47

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0150_C.bam
    Commands
    Outputs
    • data/ubam/PN0150_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (14.808 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0150_C.reverted.bam
    • data/ubam/PN0150_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0150_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:48 (0.056 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0150_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0150_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.672 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0150_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:12 (0.698 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:35 (22.495 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:35 - 2016-5-16 11:17:1 (26.450 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:1 - 2016-5-16 11:17:2 (1.093 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:3 - 2016-5-16 11:17:5 (2.400 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.810 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:7 (0.749 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.938 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:9 (0.768 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.386 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:28 (17.010 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21339
    Outputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:28 - 2016-5-16 11:19:37 (2 minutes, 8.960 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21499
    Outputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:19:37 (0.051 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:19:37 (0.012 seconds)

    Branch 48

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0192_C.bam
    Commands
    Outputs
    • data/ubam/PN0192_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.925 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0192_C.reverted.bam
    • data/ubam/PN0192_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0192_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.970 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0192_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0192_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.628 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0192_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.244 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (23.903 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.197 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.664 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.798 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.811 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.859 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.062 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.812 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.947 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.333 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21395
    Outputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:27:56 (10 minutes, 16.052 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21679
    Outputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:56 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:56 (0.008 seconds)

    Branch 49

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0117_C.bam
    Commands
    Outputs
    • data/ubam/PN0117_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.919 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0117_C.reverted.bam
    • data/ubam/PN0117_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0117_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.570 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0117_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0117_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (21.998 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0117_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.458 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:47 (27.303 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.230 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.753 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.865 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.062 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.868 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.471 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.800 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:18 - 2016-5-16 11:17:20 (2.871 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:20 - 2016-5-16 11:17:47 (26.794 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21479
    Outputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:47 - 2016-5-16 11:39:0 (21 minutes, 12.644 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21928
    Outputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:39:0 (0.060 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:39:0 (0.012 seconds)

    Branch 50

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0015_C.bam
    Commands
    Outputs
    • data/ubam/PN0015_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.421 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0015_C.reverted.bam
    • data/ubam/PN0015_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0015_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.405 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0015_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0015_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:16:17 (22.382 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0015_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.434 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:44 (25.777 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.648 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.737 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.499 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.737 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.780 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.096 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.316 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.120 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (26.199 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21443
    Outputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:33:45 (16 minutes, 4.638 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21814
    Outputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:33:45 (0.055 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:33:45 (0.007 seconds)

    Branch 51

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0145_C.bam
    Commands
    Outputs
    • data/ubam/PN0145_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.090 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0145_C.reverted.bam
    • data/ubam/PN0145_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0145_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (1.790 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0145_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0145_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:20 (23.218 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0145_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.446 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:22 - 2016-5-16 11:16:49 (26.298 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:49 - 2016-5-16 11:17:10 (21.144 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:10 (0.745 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:11 (0.824 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.637 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 (0.815 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.015 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:19 (3.123 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:19 - 2016-5-16 11:17:21 (2.222 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:21 - 2016-5-16 11:17:47 (26.261 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21481
    Outputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:47 - 2016-5-16 11:39:17 (21 minutes, 30.176 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21931
    Outputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:39:17 (0.055 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:39:17 (0.012 seconds)

    Branch 52

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0187_C.bam
    Commands
    Outputs
    • data/ubam/PN0187_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:53 (19.236 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0187_C.reverted.bam
    • data/ubam/PN0187_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0187_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.403 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0187_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0187_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.771 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0187_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.689 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.319 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:6 (23.838 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:6 (0.968 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:7 (0.556 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.842 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.607 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.175 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.956 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.070 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (24.552 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21390
    Outputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:26:10 (8 minutes, 32.689 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21640
    Outputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:26:10 (0.053 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:26:10 (0.013 seconds)

    Branch 53

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0085_C.bam
    Commands
    Outputs
    • data/ubam/PN0085_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.581 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0085_C.reverted.bam
    • data/ubam/PN0085_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0085_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.418 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0085_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0085_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.535 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0085_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.183 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.752 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.097 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.816 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.564 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.897 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.017 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.298 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.761 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.590 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (25.573 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21430
    Outputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:31:28 (13 minutes, 46.972 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21763
    Outputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:28 (0.038 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:28 (0.008 seconds)

    Branch 54

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0058_Cx.bam
    Commands
    Outputs
    • data/ubam/PN0058_Cx.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.415 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0058_Cx.reverted.bam
    • data/ubam/PN0058_Cx.reverted.bam
    Commands
    Outputs
    • data/qc/PN0058_Cx.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:47 (0.093 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0058_Cx.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0058_Cx.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.971 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0058_Cx.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:12 (0.878 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:35 (22.247 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:35 - 2016-5-16 11:17:0 (25.135 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:0 - 2016-5-16 11:17:1 (1.078 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:1 - 2016-5-16 11:17:2 (1.364 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:2 - 2016-5-16 11:17:4 (1.800 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (2.050 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.113 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:7 - 2016-5-16 11:17:9 (1.021 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.064 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:12 (2.222 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21334
    Outputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:18:50 (1 minutes, 38.017 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21487
    Outputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:18:50 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:18:50 (0.009 seconds)

    Branch 55

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0129_C.bam
    Commands
    Outputs
    • data/ubam/PN0129_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.701 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0129_C.reverted.bam
    • data/ubam/PN0129_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0129_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.336 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0129_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0129_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.287 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0129_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.650 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.377 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.470 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.852 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.632 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.400 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.624 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.303 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.121 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.609 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (27.027 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21452
    Outputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:34:18 (16 minutes, 35.941 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21823
    Outputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:34:18 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:34:18 (0.008 seconds)

    Branch 56

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0102_C.bam
    Commands
    Outputs
    • data/ubam/PN0102_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.842 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0102_C.reverted.bam
    • data/ubam/PN0102_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0102_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.032 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0102_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0102_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:20 (24.340 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0102_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.168 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:22 - 2016-5-16 11:16:47 (24.918 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (21.469 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.609 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.590 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.820 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.389 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.297 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.714 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.487 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.640 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21420
    Outputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:30:4 (12 minutes, 20.175 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21724
    Outputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:30:4 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:30:4 (0.007 seconds)

    Branch 57

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0165_C.bam
    Commands
    Outputs
    • data/ubam/PN0165_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.271 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0165_C.reverted.bam
    • data/ubam/PN0165_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0165_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.804 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0165_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0165_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.684 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0165_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.497 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.089 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.000 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.551 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.721 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.934 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.674 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.030 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.315 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.014 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.171 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21385
    Outputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:27:19 (9 minutes, 39.492 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21661
    Outputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:19 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:19 (0.008 seconds)

    Branch 58

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0020_C.bam
    Commands
    Outputs
    • data/ubam/PN0020_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.278 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0020_C.reverted.bam
    • data/ubam/PN0020_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0020_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.389 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0020_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0020_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (21.893 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0020_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (2.191 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:46 (24.877 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.536 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.636 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.788 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.713 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.934 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.938 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.270 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:18 (2.863 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:18 - 2016-5-16 11:17:45 (27.614 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21475
    Outputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:45 - 2016-5-16 11:37:33 (19 minutes, 47.999 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21893
    Outputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:33 (0.040 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:33 (0.011 seconds)

    Branch 59

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0122_C.bam
    Commands
    Outputs
    • data/ubam/PN0122_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.290 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0122_C.reverted.bam
    • data/ubam/PN0122_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0122_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.247 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0122_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0122_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.137 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0122_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.404 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.759 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:7 (22.851 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.743 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.553 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.608 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.662 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.807 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.996 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 (0.901 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:39 (26.349 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21446
    Outputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:34:43 (17 minutes, 3.823 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21838
    Outputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:34:43 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:34:43 (0.007 seconds)

    Branch 60

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0109_C.bam
    Commands
    Outputs
    • data/ubam/PN0109_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:53 (19.559 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0109_C.reverted.bam
    • data/ubam/PN0109_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0109_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.477 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0109_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0109_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.905 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0109_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.345 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.239 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:40 - 2016-5-16 11:17:5 (24.810 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.705 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:7 (0.859 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.659 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.576 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.916 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:10 (0.811 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 (0.989 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:35 (23.150 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21349
    Outputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:35 - 2016-5-16 11:21:10 (3 minutes, 35.163 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21529
    Outputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:21:10 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:21:10 (0.008 seconds)

    Branch 61

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0105_C.bam
    Commands
    Outputs
    • data/ubam/PN0105_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.431 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0105_C.reverted.bam
    • data/ubam/PN0105_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0105_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.324 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0105_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0105_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.556 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0105_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.165 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:46 (24.870 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (23.437 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.756 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.563 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.722 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.287 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.224 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.120 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.832 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.525 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21434
    Outputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:32:34 (14 minutes, 50.320 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21790
    Outputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:32:34 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:32:34 (0.008 seconds)

    Branch 62

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0007_C.bam
    Commands
    Outputs
    • data/ubam/PN0007_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.744 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0007_C.reverted.bam
    • data/ubam/PN0007_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0007_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.079 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0007_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0007_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.905 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0007_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.362 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.596 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.865 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.424 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.672 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.846 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.347 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.201 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.931 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.068 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (26.567 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21485
    Outputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:37:53 (20 minutes, 12.366 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21913
    Outputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:55 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:55 (0.007 seconds)

    Branch 63

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0040_C.bam
    Commands
    Outputs
    • data/ubam/PN0040_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.439 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0040_C.reverted.bam
    • data/ubam/PN0040_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0040_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.469 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0040_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0040_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (22.769 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0040_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.307 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (24.594 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.434 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.827 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.553 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.782 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.724 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.310 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.968 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.937 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (26.176 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21455
    Outputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:34:37 (16 minutes, 54.664 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21832
    Outputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:34:37 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:34:37 (0.007 seconds)

    Branch 64

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0082_C.bam
    Commands
    Outputs
    • data/ubam/PN0082_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.962 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0082_C.reverted.bam
    • data/ubam/PN0082_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0082_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.208 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0082_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0082_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.546 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0082_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.533 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.061 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (25.019 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.846 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.840 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.716 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.819 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.424 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.889 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 (0.956 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:40 (26.961 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21425
    Outputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:30:49 (13 minutes, 8.897 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21740
    Outputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:30:49 (0.037 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:30:49 (0.008 seconds)

    Branch 65

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0169_C.bam
    Commands
    Outputs
    • data/ubam/PN0169_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.462 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0169_C.reverted.bam
    • data/ubam/PN0169_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0169_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.676 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0169_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0169_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.355 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0169_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.023 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.204 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.397 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.792 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.755 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.706 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.531 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.351 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.736 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.911 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (24.697 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21410
    Outputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:29:51 (12 minutes, 12.419 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21718
    Outputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:29:51 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:29:51 (0.008 seconds)

    Branch 66

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0180_C.bam
    Commands
    Outputs
    • data/ubam/PN0180_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.079 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0180_C.reverted.bam
    • data/ubam/PN0180_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0180_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.911 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0180_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0180_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.154 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0180_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:17 (1.430 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:42 (24.817 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:42 - 2016-5-16 11:17:6 (24.065 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.448 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.686 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.626 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.821 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.827 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.453 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.144 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:36 (23.660 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21381
    Outputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:36 - 2016-5-16 11:26:47 (9 minutes, 10.582 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21649
    Outputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:26:47 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:26:47 (0.008 seconds)

    Branch 67

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0142_C.bam
    Commands
    Outputs
    • data/ubam/PN0142_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.339 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0142_C.reverted.bam
    • data/ubam/PN0142_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0142_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.776 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0142_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0142_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.850 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0142_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.595 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (26.684 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.516 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.437 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.349 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.915 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.921 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.230 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.137 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.044 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (26.200 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21437
    Outputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:32:29 (14 minutes, 46.529 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21784
    Outputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:32:29 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:32:29 (0.008 seconds)

    Branch 68

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0125_C.bam
    Commands
    Outputs
    • data/ubam/PN0125_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.689 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0125_C.reverted.bam
    • data/ubam/PN0125_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0125_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.178 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0125_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0125_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.024 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0125_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.376 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.157 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.237 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.683 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.723 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.674 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.820 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:12 (1.160 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.007 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.852 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (27.143 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21360
    Outputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:22:8 (4 minutes, 26.942 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21553
    Outputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:22:8 (0.051 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:22:8 (0.008 seconds)

    Branch 69

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0027_C.bam
    Commands
    Outputs
    • data/ubam/PN0027_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.260 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0027_C.reverted.bam
    • data/ubam/PN0027_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0027_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.797 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0027_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0027_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.558 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0027_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.472 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.106 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:40 - 2016-5-16 11:17:6 (25.535 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.434 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:7 (0.757 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.543 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.792 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.257 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.323 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 (0.578 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:36 (23.805 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21359
    Outputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:36 - 2016-5-16 11:23:7 (5 minutes, 30.850 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21574
    Outputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:23:7 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:23:7 (0.008 seconds)

    Branch 70

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0089_C.bam
    Commands
    Outputs
    • data/ubam/PN0089_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.606 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0089_C.reverted.bam
    • data/ubam/PN0089_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0089_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.202 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0089_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0089_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.429 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0089_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.136 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.894 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.131 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.738 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.970 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.752 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.922 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.926 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.894 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.935 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:45 (28.818 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21439
    Outputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:45 - 2016-5-16 11:31:49 (14 minutes, 4.233 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21772
    Outputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:49 (0.031 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:49 (0.008 seconds)

    Branch 71

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0162_C.bam
    Commands
    Outputs
    • data/ubam/PN0162_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.555 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0162_C.reverted.bam
    • data/ubam/PN0162_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0162_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.980 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0162_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0162_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.721 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0162_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:21 (2.292 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:45 (24.465 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.315 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.715 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.469 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.750 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.943 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.394 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.548 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:19 (3.762 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:19 - 2016-5-16 11:17:46 (27.846 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21451
    Outputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:47 - 2016-5-16 11:34:25 (16 minutes, 38.404 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21829
    Outputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:34:25 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:34:25 (0.021 seconds)

    Branch 72

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0149_C.bam
    Commands
    Outputs
    • data/ubam/PN0149_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.568 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0149_C.reverted.bam
    • data/ubam/PN0149_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0149_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.993 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0149_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0149_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.645 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0149_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.089 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.181 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.070 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.694 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.849 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.594 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.748 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.705 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.987 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.629 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (25.081 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21352
    Outputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:22:31 (4 minutes, 52.997 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21562
    Outputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:22:31 (0.031 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:22:31 (0.007 seconds)

    Branch 73

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0115_C.bam
    Commands
    Outputs
    • data/ubam/PN0115_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.775 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0115_C.reverted.bam
    • data/ubam/PN0115_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0115_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.439 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0115_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0115_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:17 (21.009 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0115_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (2.059 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.494 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.710 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.795 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.779 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.927 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.869 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.964 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.990 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.496 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (27.600 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21465
    Outputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:36:31 (18 minutes, 46.646 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21868
    Outputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:36:31 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:36:31 (0.007 seconds)

    Branch 74

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0179_C.bam
    Commands
    Outputs
    • data/ubam/PN0179_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.749 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0179_C.reverted.bam
    • data/ubam/PN0179_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0179_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.334 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0179_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0179_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.390 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0179_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:22 (2.308 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:22 - 2016-5-16 11:16:47 (25.657 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:48 - 2016-5-16 11:17:10 (22.553 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:10 (0.603 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:11 (0.797 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.787 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 (0.681 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.783 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:18 (2.793 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:18 - 2016-5-16 11:17:21 (2.804 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:21 - 2016-5-16 11:17:47 (26.266 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21473
    Outputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:47 - 2016-5-16 11:38:40 (20 minutes, 52.600 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21919
    Outputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:38:40 (0.054 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:38:40 (0.012 seconds)

    Branch 75

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0190_C.bam
    Commands
    Outputs
    • data/ubam/PN0190_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.969 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0190_C.reverted.bam
    • data/ubam/PN0190_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0190_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.201 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0190_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0190_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.602 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0190_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.402 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.773 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.024 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.746 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.418 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.759 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.004 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.938 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.132 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.297 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (26.317 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21412
    Outputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:29:58 (12 minutes, 16.729 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21721
    Outputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:29:58 (0.040 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:29:58 (0.010 seconds)

    Branch 76

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0037_C.bam
    Commands
    Outputs
    • data/ubam/PN0037_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.434 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0037_C.reverted.bam
    • data/ubam/PN0037_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0037_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:47 (0.089 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0037_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0037_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.954 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0037_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:12 (0.087 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:34 (21.948 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:34 - 2016-5-16 11:16:58 (24.184 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:16:58 (0.055 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:16:58 (0.888 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:59 - 2016-5-16 11:17:0 (1.438 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:1 - 2016-5-16 11:17:2 (1.357 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:2 - 2016-5-16 11:17:5 (3.322 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.865 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.067 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:8 - 2016-5-16 11:17:12 (4.031 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21333
    Outputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:19:32 (2 minutes, 19.596 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21496
    Outputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:19:32 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:19:32 (0.008 seconds)

    Branch 77

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0135_C.bam
    Commands
    Outputs
    • data/ubam/PN0135_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:53 (19.582 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0135_C.reverted.bam
    • data/ubam/PN0135_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0135_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.241 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0135_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0135_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.849 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0135_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.473 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.986 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.414 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.634 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.876 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.630 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.751 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.787 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.149 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.320 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.247 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21369
    Outputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:24:26 (6 minutes, 46.347 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21593
    Outputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:24:26 (0.052 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:24:26 (0.009 seconds)

    Branch 78

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0159_C.bam
    Commands
    Outputs
    • data/ubam/PN0159_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:46 (13.268 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0159_C.reverted.bam
    • data/ubam/PN0159_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0159_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:46 - 2016-5-16 11:15:48 (1.130 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0159_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0159_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.981 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0159_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:13 (1.450 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:13 - 2016-5-16 11:16:36 (23.267 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:36 - 2016-5-16 11:17:2 (25.943 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:2 - 2016-5-16 11:17:5 (2.715 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:6 (1.539 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.128 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.790 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.975 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.125 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.377 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:35 (22.804 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21348
    Outputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:35 - 2016-5-16 11:21:48 (4 minutes, 13.332 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21547
    Outputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:21:48 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:21:49 (0.007 seconds)

    Branch 79

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0172_C.bam
    Commands
    Outputs
    • data/ubam/PN0172_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.152 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0172_C.reverted.bam
    • data/ubam/PN0172_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0172_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.911 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0172_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0172_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (22.406 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0172_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.567 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (25.641 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:8 (22.392 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.838 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.906 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.807 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.861 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.024 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.128 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.370 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.945 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21454
    Outputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:34:4 (16 minutes, 20.167 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21820
    Outputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:34:4 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:34:4 (0.008 seconds)

    Branch 80

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0099_C.bam
    Commands
    Outputs
    • data/ubam/PN0099_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.046 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0099_C.reverted.bam
    • data/ubam/PN0099_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0099_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.940 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0099_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0099_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.321 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0099_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.886 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.019 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.262 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.704 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.852 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.666 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.780 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.000 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.022 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.881 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.184 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21375
    Outputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:24:49 (7 minutes, 10.963 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21598
    Outputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:24:49 (0.039 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:24:49 (0.008 seconds)

    Branch 81

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0057_C.bam
    Commands
    Outputs
    • data/ubam/PN0057_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.185 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0057_C.reverted.bam
    • data/ubam/PN0057_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0057_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (1.916 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0057_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0057_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:20 (22.774 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0057_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.282 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:22 - 2016-5-16 11:16:47 (24.794 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.207 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.675 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.939 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.711 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.910 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.140 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.083 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:19 (3.474 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:19 - 2016-5-16 11:17:46 (27.084 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21480
    Outputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:40:19 (22 minutes, 32.710 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21937
    Outputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:40:19 (0.054 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:40:19 (0.013 seconds)

    Branch 82

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0155_C.bam
    Commands
    Outputs
    • data/ubam/PN0155_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:49 (15.815 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0155_C.reverted.bam
    • data/ubam/PN0155_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0155_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:49 - 2016-5-16 11:15:51 (1.719 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0155_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0155_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:51 - 2016-5-16 11:16:12 (20.858 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0155_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:12 (0.081 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:35 (23.096 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:35 - 2016-5-16 11:17:1 (26.471 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:1 - 2016-5-16 11:17:4 (2.170 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (2.103 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.402 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:7 (0.797 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.136 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.148 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:10 (0.492 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:32 (20.713 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21342
    Outputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:32 - 2016-5-16 11:20:29 (2 minutes, 57.769 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21520
    Outputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:20:29 (0.053 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:20:30 (0.012 seconds)

    Branch 83

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0112_C.bam
    Commands
    Outputs
    • data/ubam/PN0112_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.294 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0112_C.reverted.bam
    • data/ubam/PN0112_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0112_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.972 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0112_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0112_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.652 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0112_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.896 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.547 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:8 (24.329 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.776 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.677 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.678 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.957 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.708 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.897 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.393 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (24.427 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21373
    Outputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:25:6 (7 minutes, 28.523 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21607
    Outputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:6 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:6 (0.009 seconds)

    Branch 84

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0010_C.bam
    Commands
    Outputs
    • data/ubam/PN0010_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.024 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0010_C.reverted.bam
    • data/ubam/PN0010_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0010_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.175 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0010_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0010_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.235 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0010_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.946 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:47 (26.708 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:8 (21.521 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.730 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.714 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.697 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.891 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.252 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.277 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.036 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (26.605 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21448
    Outputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:34:38 (16 minutes, 55.319 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21835
    Outputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:34:38 (0.060 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:34:38 (0.011 seconds)

    Branch 85

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0077_C.bam
    Commands
    Outputs
    • data/ubam/PN0077_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.910 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0077_C.reverted.bam
    • data/ubam/PN0077_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0077_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.129 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0077_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0077_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.171 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0077_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.278 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (26.666 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.151 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.702 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.854 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.716 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.020 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.886 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.187 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.357 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:46 (28.826 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21468
    Outputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:36:33 (18 minutes, 47.297 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21871
    Outputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:36:33 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:36:33 (0.009 seconds)

    Branch 86

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0119_C.bam
    Commands
    Outputs
    • data/ubam/PN0119_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.574 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0119_C.reverted.bam
    • data/ubam/PN0119_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0119_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.142 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0119_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0119_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.880 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0119_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.073 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.358 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.990 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.755 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.514 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.829 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.660 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.104 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.090 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.490 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (27.032 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21442
    Outputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:33:40 (15 minutes, 57.422 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21811
    Outputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:33:40 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:33:40 (0.008 seconds)

    Branch 87

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0030_C.bam
    Commands
    Outputs
    • data/ubam/PN0030_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.913 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0030_C.reverted.bam
    • data/ubam/PN0030_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0030_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.190 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0030_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0030_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:17 (21.744 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0030_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 (0.877 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:39 (20.917 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:39 - 2016-5-16 11:17:5 (25.992 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.312 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:7 (0.537 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:7 (0.735 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.860 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.159 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:10 (0.506 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 (0.545 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:32 (20.065 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21340
    Outputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:32 - 2016-5-16 11:18:16 (44.211 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21402
    Outputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:18:16 (0.096 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:18:16 (0.019 seconds)

    Branch 88

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0101_C.bam
    Commands
    Outputs
    • data/ubam/PN0101_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.774 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0101_C.reverted.bam
    • data/ubam/PN0101_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0101_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.438 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0101_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0101_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (21.613 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0101_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.987 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.335 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.668 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.763 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.758 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.596 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.715 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.504 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.041 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.544 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (25.184 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21404
    Outputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:28:53 (11 minutes, 12.750 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21698
    Outputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:28:53 (0.067 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:28:53 (0.013 seconds)

    Branch 89

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0028_C.bam
    Commands
    Outputs
    • data/ubam/PN0028_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.425 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0028_C.reverted.bam
    • data/ubam/PN0028_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0028_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.228 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0028_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0028_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.089 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0028_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.763 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (25.785 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:8 (22.205 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.873 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.689 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.582 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.405 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.067 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.333 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.473 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (25.485 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21405
    Outputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:28:11 (10 minutes, 28.956 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21688
    Outputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:28:11 (0.050 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:28:11 (0.008 seconds)

    Branch 90

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0003_C.bam
    Commands
    Outputs
    • data/ubam/PN0003_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.102 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0003_C.reverted.bam
    • data/ubam/PN0003_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0003_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.049 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0003_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0003_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.264 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0003_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (2.162 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:48 (26.584 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:48 - 2016-5-16 11:17:9 (21.575 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.562 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.831 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.420 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.819 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.743 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.034 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.698 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:45 (28.038 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21467
    Outputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:45 - 2016-5-16 11:36:48 (19 minutes, 3.698 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21882
    Outputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:36:48 (0.042 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:36:49 (0.008 seconds)

    Branch 91

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0044_C.bam
    Commands
    Outputs
    • data/ubam/PN0044_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:53 (19.637 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0044_C.reverted.bam
    • data/ubam/PN0044_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0044_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.552 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0044_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0044_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.756 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0044_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.586 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (23.927 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (24.621 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.398 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.754 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.746 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.719 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.835 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.813 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 (0.911 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:36 (23.091 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21345
    Outputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:36 - 2016-5-16 11:19:55 (2 minutes, 19.092 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21511
    Outputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:19:55 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:19:55 (0.008 seconds)

    Branch 92

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0086_C.bam
    Commands
    Outputs
    • data/ubam/PN0086_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.425 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0086_C.reverted.bam
    • data/ubam/PN0086_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0086_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.985 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0086_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0086_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (20.956 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0086_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.754 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.530 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.226 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.625 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.768 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.754 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.919 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.070 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.117 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.387 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (27.003 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21393
    Outputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:27:11 (9 minutes, 29.463 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21655
    Outputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:11 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:11 (0.008 seconds)

    Branch 93

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0184_C.bam
    Commands
    Outputs
    • data/ubam/PN0184_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.984 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0184_C.reverted.bam
    • data/ubam/PN0184_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0184_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 (0.875 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0184_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0184_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:17 (21.811 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0184_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.388 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (26.480 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.525 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.697 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.607 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.771 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.558 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.937 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.078 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.835 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.535 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21372
    Outputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:25:4 (7 minutes, 24.871 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21604
    Outputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:4 (0.047 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:4 (0.010 seconds)

    Branch 94

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0121_C.bam
    Commands
    Outputs
    • data/ubam/PN0121_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.613 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0121_C.reverted.bam
    • data/ubam/PN0121_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0121_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.145 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0121_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0121_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.603 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0121_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 (0.977 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.341 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:8 (22.830 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.650 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.938 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.854 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.928 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.958 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.317 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.442 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (25.720 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21459
    Outputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:36:26 (18 minutes, 42.974 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21865
    Outputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:36:26 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:36:26 (0.008 seconds)

    Branch 95

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0023_C.bam
    Commands
    Outputs
    • data/ubam/PN0023_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.251 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0023_C.reverted.bam
    • data/ubam/PN0023_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0023_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.112 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0023_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0023_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.251 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0023_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.258 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.498 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.108 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.613 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.542 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.681 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.682 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.923 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.996 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:14 (1.113 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.905 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21407
    Outputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:32:25 (14 minutes, 45.194 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21781
    Outputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:32:25 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:32:25 (0.008 seconds)

    Branch 96

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0008_C.bam
    Commands
    Outputs
    • data/ubam/PN0008_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.680 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0008_C.reverted.bam
    • data/ubam/PN0008_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0008_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.927 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0008_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0008_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.709 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0008_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.816 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.100 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:6 (23.337 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.213 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.876 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.866 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.693 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.072 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.330 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.857 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:40 (26.951 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21426
    Outputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:31:20 (13 minutes, 39.630 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21754
    Outputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:20 (0.052 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:20 (0.012 seconds)

    Branch 97

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0166_C.bam
    Commands
    Outputs
    • data/ubam/PN0166_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.407 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0166_C.reverted.bam
    • data/ubam/PN0166_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0166_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:47 (0.091 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0166_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0166_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:8 (20.064 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0166_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:8 (0.483 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:8 - 2016-5-16 11:16:36 (28.012 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:36 - 2016-5-16 11:16:59 (23.014 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:16:59 - 2016-5-16 11:17:0 (1.143 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:0 - 2016-5-16 11:17:2 (1.441 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:2 - 2016-5-16 11:17:4 (1.618 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (1.802 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (2.275 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.183 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:9 (0.885 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:13 (3.095 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21336
    Outputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:20:8 (2 minutes, 54.499 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21514
    Outputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:20:8 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:20:8 (0.009 seconds)

    Branch 98

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0141_C.bam
    Commands
    Outputs
    • data/ubam/PN0141_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.570 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0141_C.reverted.bam
    • data/ubam/PN0141_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0141_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:47 (0.097 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0141_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0141_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.942 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0141_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:12 (0.080 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:35 (23.042 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:35 - 2016-5-16 11:17:0 (25.498 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:0 - 2016-5-16 11:17:1 (1.134 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:2 - 2016-5-16 11:17:3 (1.145 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:3 - 2016-5-16 11:17:4 (1.067 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (1.836 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.352 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:7 (0.983 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:8 (0.986 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:12 (3.000 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21332
    Outputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:19:52 (2 minutes, 40.182 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21508
    Outputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:19:52 (0.055 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:19:52 (0.013 seconds)

    Branch 99

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0183_C.bam
    Commands
    Outputs
    • data/ubam/PN0183_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.325 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0183_C.reverted.bam
    • data/ubam/PN0183_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0183_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.958 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0183_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0183_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.845 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0183_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.369 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.833 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.147 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.737 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.287 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.025 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.339 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.153 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.195 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.417 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (27.323 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21418
    Outputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:29:15 (11 minutes, 31.198 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21712
    Outputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:29:15 (0.044 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:29:15 (0.009 seconds)

    Branch 100

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0081_C.bam
    Commands
    Outputs
    • data/ubam/PN0081_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.959 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0081_C.reverted.bam
    • data/ubam/PN0081_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0081_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.906 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0081_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0081_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.018 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0081_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.321 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:41 (22.652 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:41 - 2016-5-16 11:17:7 (25.513 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.812 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.742 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.660 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.904 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.624 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.574 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.078 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:36 (23.662 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21356
    Outputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:36 - 2016-5-16 11:21:12 (3 minutes, 35.986 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21532
    Outputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:21:12 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:21:13 (0.009 seconds)

    Branch 101

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0043_C.bam
    Commands
    Outputs
    • data/ubam/PN0043_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.370 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0043_C.reverted.bam
    • data/ubam/PN0043_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0043_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.732 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0043_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0043_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (21.780 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0043_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (2.304 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:47 (25.300 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.511 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.530 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.623 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.727 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.888 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.963 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.101 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.208 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (26.766 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21409
    Outputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:28:25 (10 minutes, 41.460 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21691
    Outputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:28:25 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:28:25 (0.007 seconds)

    Branch 102

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0004_C.bam
    Commands
    Outputs
    • data/ubam/PN0004_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.726 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0004_C.reverted.bam
    • data/ubam/PN0004_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0004_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.137 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0004_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0004_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.101 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0004_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.517 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.964 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.952 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.884 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.653 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.940 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.412 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.391 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.984 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.191 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (25.772 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21398
    Outputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:27:27 (9 minutes, 46.219 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21665
    Outputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:27 (0.042 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:27 (0.007 seconds)

    Branch 103

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0161_C.bam
    Commands
    Outputs
    • data/ubam/PN0161_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.382 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0161_C.reverted.bam
    • data/ubam/PN0161_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0161_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.077 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0161_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0161_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.112 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0161_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.392 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (24.885 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.487 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.691 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.749 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.932 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.863 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.030 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.626 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:16 (2.183 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (26.528 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21389
    Outputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:26:11 (8 minutes, 28.368 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21643
    Outputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:26:11 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:26:11 (0.008 seconds)

    Branch 104

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0188_C.bam
    Commands
    Outputs
    • data/ubam/PN0188_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.077 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0188_C.reverted.bam
    • data/ubam/PN0188_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0188_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.321 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0188_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0188_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.289 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0188_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.212 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:22 - 2016-5-16 11:16:47 (25.398 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:10 (22.356 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:10 (0.833 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:11 (0.679 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.810 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.660 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 (0.627 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.460 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:20 (3.424 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:20 - 2016-5-16 11:17:46 (26.711 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21474
    Outputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:36:39 (18 minutes, 52.854 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21877
    Outputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:36:39 (0.036 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:36:39 (0.008 seconds)

    Branch 105

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0063_C.bam
    Commands
    Outputs
    • data/ubam/PN0063_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.829 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0063_C.reverted.bam
    • data/ubam/PN0063_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0063_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.827 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0063_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0063_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.367 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0063_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.225 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.864 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.312 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.834 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.752 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.679 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.774 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.940 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.287 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.941 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.134 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21353
    Outputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:21:19 (3 minutes, 41.294 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21535
    Outputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:21:19 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:21:19 (0.008 seconds)

    Branch 106

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0126_C.bam
    Commands
    Outputs
    • data/ubam/PN0126_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.615 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0126_C.reverted.bam
    • data/ubam/PN0126_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0126_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.348 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0126_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0126_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.437 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0126_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.581 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.992 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.379 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.593 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.855 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.589 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.763 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.102 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.032 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.812 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (26.745 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21464
    Outputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:36:3 (18 minutes, 19.907 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21859
    Outputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:36:3 (0.032 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:36:3 (0.007 seconds)

    Branch 107

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0078_C.bam
    Commands
    Outputs
    • data/ubam/PN0078_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.770 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0078_C.reverted.bam
    • data/ubam/PN0078_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0078_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.179 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0078_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0078_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.577 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0078_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.686 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.076 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.713 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.670 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.876 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.818 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.790 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.350 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.900 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.438 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (26.018 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21396
    Outputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:27:27 (9 minutes, 45.931 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21666
    Outputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:27 (0.037 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:27 (0.008 seconds)

    Branch 108

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0091_C.bam
    Commands
    Outputs
    • data/ubam/PN0091_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.599 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0091_C.reverted.bam
    • data/ubam/PN0091_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0091_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.585 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0091_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0091_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.156 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0091_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.799 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:47 (26.128 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.039 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.890 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.366 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.106 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.669 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 (0.998 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.669 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (1.956 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (25.997 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21432
    Outputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:31:14 (13 minutes, 30.425 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21751
    Outputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:14 (0.031 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:14 (0.008 seconds)

    Branch 109

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0151_C.bam
    Commands
    Outputs
    • data/ubam/PN0151_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.354 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0151_C.reverted.bam
    • data/ubam/PN0151_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0151_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.011 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0151_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0151_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.998 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0151_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.429 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (23.897 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:8 (24.424 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.625 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.424 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.986 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.887 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.537 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.018 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.481 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:43 (27.750 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21449
    Outputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:34:55 (17 minutes, 11.982 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21844
    Outputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:34:55 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:34:55 (0.008 seconds)

    Branch 110

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0116_C.bam
    Commands
    Outputs
    • data/ubam/PN0116_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.398 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0116_C.reverted.bam
    • data/ubam/PN0116_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0116_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.592 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0116_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0116_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.007 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0116_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.802 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.367 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.216 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.688 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.672 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.794 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.511 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.813 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.326 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:14 (1.174 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.221 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21399
    Outputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:29:0 (11 minutes, 20.221 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21703
    Outputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:29:0 (0.037 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:29:0 (0.011 seconds)

    Branch 111

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0014_C.bam
    Commands
    Outputs
    • data/ubam/PN0014_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.785 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0014_C.reverted.bam
    • data/ubam/PN0014_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0014_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.079 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0014_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0014_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.764 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0014_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.953 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (26.295 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.988 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.806 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.920 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.395 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.851 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.029 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.756 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.581 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (26.850 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21445
    Outputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:33:8 (15 minutes, 25.481 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21796
    Outputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:33:8 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:33:8 (0.008 seconds)

    Branch 112

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0073_C.bam
    Commands
    Outputs
    • data/ubam/PN0073_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (15.079 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0073_C.reverted.bam
    • data/ubam/PN0073_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0073_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:48 (0.089 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0073_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0073_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:16:8 (19.982 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0073_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:8 - 2016-5-16 11:16:12 (3.329 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:12 - 2016-5-16 11:16:33 (21.826 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:33 - 2016-5-16 11:16:58 (24.650 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:16:58 (0.096 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:16:58 (0.936 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:59 - 2016-5-16 11:17:1 (1.475 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:1 - 2016-5-16 11:17:3 (2.054 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:3 - 2016-5-16 11:17:6 (2.955 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.939 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.179 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:12 (3.387 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21331
    Outputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:19:27 (2 minutes, 14.909 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21493
    Outputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:19:27 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:19:27 (0.008 seconds)

    Branch 113

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0171_C.bam
    Commands
    Outputs
    • data/ubam/PN0171_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.275 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0171_C.reverted.bam
    • data/ubam/PN0171_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0171_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:58 (2.652 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0171_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0171_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:58 - 2016-5-16 11:16:21 (23.525 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0171_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:23 (1.505 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:23 - 2016-5-16 11:16:45 (22.689 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.420 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.688 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.653 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.819 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.686 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.633 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.001 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.750 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:43 (27.920 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21400
    Outputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:43 - 2016-5-16 11:29:10 (11 minutes, 26.365 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21709
    Outputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:29:10 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:29:10 (0.007 seconds)

    Branch 114

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0013_C.bam
    Commands
    Outputs
    • data/ubam/PN0013_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.296 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0013_C.reverted.bam
    • data/ubam/PN0013_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0013_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.754 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0013_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0013_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.267 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0013_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 (0.869 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:44 (26.356 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:9 (24.456 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.715 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.468 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.541 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.062 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.133 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.784 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (3.017 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:45 (27.610 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21472
    Outputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:45 - 2016-5-16 11:37:8 (19 minutes, 23.608 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21889
    Outputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:8 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:8 (0.008 seconds)

    Branch 115

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0111_C.bam
    Commands
    Outputs
    • data/ubam/PN0111_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.210 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0111_C.reverted.bam
    • data/ubam/PN0111_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0111_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.547 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0111_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0111_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (21.990 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0111_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.924 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:46 (24.533 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (23.442 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.613 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.773 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.626 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.934 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.240 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.931 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:20 (3.736 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:20 - 2016-5-16 11:17:46 (26.867 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21478
    Outputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:38:12 (20 minutes, 25.894 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21916
    Outputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:38:12 (0.067 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:38:12 (0.014 seconds)

    Branch 116

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0156_C.bam
    Commands
    Outputs
    • data/ubam/PN0156_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.974 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0156_C.reverted.bam
    • data/ubam/PN0156_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0156_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.203 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0156_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0156_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.470 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0156_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.802 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (26.253 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.275 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.700 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.691 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.818 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.666 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.446 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.713 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:16 (1.547 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:46 (29.730 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21470
    Outputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:37:40 (19 minutes, 53.439 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21898
    Outputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:40 (0.054 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:40 (0.011 seconds)

    Branch 117

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0054_C.bam
    Commands
    Outputs
    • data/ubam/PN0054_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.360 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0054_C.reverted.bam
    • data/ubam/PN0054_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0054_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.821 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0054_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0054_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.216 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0054_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.169 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.010 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:40 - 2016-5-16 11:17:5 (24.781 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (2.271 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:7 (0.601 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.764 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.771 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.994 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.006 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.064 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (25.122 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21371
    Outputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:25:19 (7 minutes, 40.791 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21616
    Outputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:19 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:19 (0.009 seconds)

    Branch 118

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0131_C.bam
    Commands
    Outputs
    • data/ubam/PN0131_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (15.378 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0131_C.reverted.bam
    • data/ubam/PN0131_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0131_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:48 - 2016-5-16 11:15:51 (2.858 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0131_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0131_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:51 - 2016-5-16 11:16:13 (21.523 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0131_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:13 (0.781 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:14 - 2016-5-16 11:16:36 (22.681 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:36 - 2016-5-16 11:17:3 (26.385 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:3 - 2016-5-16 11:17:4 (1.559 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (2.043 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:6 (0.804 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:7 (0.747 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.262 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.364 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 (0.977 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:32 (20.262 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21344
    Outputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:32 - 2016-5-16 11:20:53 (3 minutes, 21.045 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21523
    Outputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:20:53 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:20:53 (0.007 seconds)

    Branch 119

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0176_C.bam
    Commands
    Outputs
    • data/ubam/PN0176_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.321 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0176_C.reverted.bam
    • data/ubam/PN0176_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0176_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.019 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0176_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0176_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.331 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0176_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.534 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.514 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:9 (23.307 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.832 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.751 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.684 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.966 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.056 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.878 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:18 (2.260 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:18 - 2016-5-16 11:17:46 (28.684 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21477
    Outputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:38:56 (21 minutes, 9.438 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21923
    Outputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:38:56 (0.051 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:38:56 (0.011 seconds)

    Branch 120

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0074_C.bam
    Commands
    Outputs
    • data/ubam/PN0074_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.152 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0074_C.reverted.bam
    • data/ubam/PN0074_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0074_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.917 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0074_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0074_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.294 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0074_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.176 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.116 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (23.552 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.519 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.605 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.581 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.780 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.210 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.516 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.940 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.700 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21406
    Outputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:28:10 (10 minutes, 30.506 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21685
    Outputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:28:10 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:28:10 (0.008 seconds)

    Branch 121

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0124_C.bam
    Commands
    Outputs
    • data/ubam/PN0124_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.780 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0124_C.reverted.bam
    • data/ubam/PN0124_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0124_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.980 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0124_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0124_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.599 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0124_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.440 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.130 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:40 - 2016-5-16 11:17:3 (23.530 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:4 - 2016-5-16 11:17:5 (1.420 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:5 (0.974 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.086 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:7 (0.729 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.079 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.379 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.241 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:34 (21.622 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21355
    Outputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:34 - 2016-5-16 11:22:48 (5 minutes, 13.936 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21568
    Outputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:22:48 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:22:48 (0.009 seconds)

    Branch 122

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0148_C.bam
    Commands
    Outputs
    • data/ubam/PN0148_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.668 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0148_C.reverted.bam
    • data/ubam/PN0148_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0148_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.166 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0148_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0148_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.122 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0148_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.974 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.522 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:8 (24.267 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.505 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.469 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.718 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.330 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.936 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.890 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.063 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:39 (25.579 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21347
    Outputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:21:25 (3 minutes, 46.090 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21541
    Outputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:21:25 (0.036 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:21:25 (0.008 seconds)

    Branch 123

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0163_C.bam
    Commands
    Outputs
    • data/ubam/PN0163_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.503 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0163_C.reverted.bam
    • data/ubam/PN0163_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0163_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.085 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0163_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0163_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.868 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0163_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.440 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:47 (27.753 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.030 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.736 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.628 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.401 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.034 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 (0.999 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.118 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:18 (2.117 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:18 - 2016-5-16 11:17:44 (25.652 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21441
    Outputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:33:57 (16 minutes, 13.741 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21817
    Outputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:33:57 (0.031 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:33:57 (0.008 seconds)

    Branch 124

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0104_C.bam
    Commands
    Outputs
    • data/ubam/PN0104_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.025 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0104_C.reverted.bam
    • data/ubam/PN0104_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0104_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.138 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0104_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0104_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.569 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0104_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.255 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.066 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:40 - 2016-5-16 11:17:7 (26.871 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.848 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.697 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.700 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.570 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.860 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.046 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.034 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (24.648 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21362
    Outputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:23:15 (5 minutes, 37.407 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21583
    Outputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:23:15 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:23:15 (0.007 seconds)

    Branch 125

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0006_C.bam
    Commands
    Outputs
    • data/ubam/PN0006_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.149 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0006_C.reverted.bam
    • data/ubam/PN0006_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0006_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.854 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0006_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0006_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:21 (23.977 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0006_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:22 (1.728 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:22 - 2016-5-16 11:16:48 (25.439 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:48 - 2016-5-16 11:17:10 (22.361 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:10 (0.364 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:11 (0.331 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.024 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 (0.865 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.292 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.522 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:20 (3.216 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:21 - 2016-5-16 11:17:47 (26.130 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21471
    Outputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:47 - 2016-5-16 11:38:56 (21 minutes, 9.241 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21924
    Outputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:38:56 (0.039 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:38:56 (0.010 seconds)

    Branch 126

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0083_C.bam
    Commands
    Outputs
    • data/ubam/PN0083_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.686 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0083_C.reverted.bam
    • data/ubam/PN0083_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0083_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.110 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0083_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0083_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.445 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0083_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:21 (2.154 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:44 (22.965 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.295 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.942 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.541 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.802 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.763 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.523 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.173 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.027 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:39 (26.049 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21379
    Outputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:25:18 (7 minutes, 38.922 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21613
    Outputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:18 (0.057 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:18 (0.013 seconds)

    Branch 127

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0041_C.bam
    Commands
    Outputs
    • data/ubam/PN0041_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.171 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0041_C.reverted.bam
    • data/ubam/PN0041_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0041_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.717 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0041_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0041_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.589 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0041_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.107 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.688 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.991 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.484 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.825 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.582 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.779 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.802 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.075 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.905 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (27.491 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21414
    Outputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:29:31 (11 minutes, 49.570 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21715
    Outputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:29:31 (0.043 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:29:31 (0.009 seconds)

    Branch 128

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0143_C.bam
    Commands
    Outputs
    • data/ubam/PN0143_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.905 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0143_C.reverted.bam
    • data/ubam/PN0143_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0143_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.163 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0143_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0143_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (22.890 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0143_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.055 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.247 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.147 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.817 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.638 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.732 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.696 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.077 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.922 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.307 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:42 (27.546 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21433
    Outputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:33:9 (15 minutes, 27.662 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21799
    Outputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:33:9 (0.036 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:33:9 (0.012 seconds)

    Branch 129

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0181_C.bam
    Commands
    Outputs
    • data/ubam/PN0181_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.428 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0181_C.reverted.bam
    • data/ubam/PN0181_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0181_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.197 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0181_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0181_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:20 (24.074 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0181_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:23 (2.952 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:23 - 2016-5-16 11:16:49 (26.606 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:49 - 2016-5-16 11:17:9 (19.689 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.762 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.644 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.428 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.814 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.154 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.228 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.861 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:45 (27.549 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21482
    Outputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:45 - 2016-5-16 11:40:5 (22 minutes, 20.108 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21934
    Outputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:40:5 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:40:5 (0.008 seconds)

    Branch 130

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0168_C.bam
    Commands
    Outputs
    • data/ubam/PN0168_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.802 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0168_C.reverted.bam
    • data/ubam/PN0168_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0168_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.720 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0168_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0168_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.386 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0168_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.480 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (26.082 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (23.254 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.677 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.666 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.323 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.888 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.980 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.483 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.252 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:45 (27.607 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21438
    Outputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:45 - 2016-5-16 11:32:4 (14 minutes, 18.877 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21778
    Outputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:32:4 (0.037 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:32:4 (0.009 seconds)

    Branch 131

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0164_C.bam
    Commands
    Outputs
    • data/ubam/PN0164_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.208 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0164_C.reverted.bam
    • data/ubam/PN0164_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0164_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.098 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0164_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0164_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (22.108 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0164_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (2.358 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:22 - 2016-5-16 11:16:49 (27.450 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:49 - 2016-5-16 11:17:8 (19.491 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.808 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.221 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.838 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.051 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.322 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.285 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.564 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (25.795 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21450
    Outputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:35:39 (17 minutes, 57.118 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21855
    Outputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:35:39 (0.046 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:35:39 (0.012 seconds)

    Branch 132

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0108_C.bam
    Commands
    Outputs
    • data/ubam/PN0108_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.721 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0108_C.reverted.bam
    • data/ubam/PN0108_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0108_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.268 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0108_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0108_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.684 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0108_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.100 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.725 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.520 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.697 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.028 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.345 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.067 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.907 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.190 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.491 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (25.938 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21424
    Outputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:31:58 (14 minutes, 16.294 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21775
    Outputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:58 (0.031 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:58 (0.007 seconds)

    Branch 133

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0186_C.bam
    Commands
    Outputs
    • data/ubam/PN0186_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.635 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0186_C.reverted.bam
    • data/ubam/PN0186_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0186_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.030 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0186_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0186_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.231 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0186_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.966 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.048 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.557 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.576 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.864 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.763 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.995 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.273 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.906 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.359 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (25.836 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21370
    Outputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:24:58 (7 minutes, 17.760 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21601
    Outputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:24:58 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:24:58 (0.012 seconds)

    Branch 134

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0084_C.bam
    Commands
    Outputs
    • data/ubam/PN0084_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.158 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0084_C.reverted.bam
    • data/ubam/PN0084_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0084_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.752 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0084_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0084_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:20 (22.718 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0084_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.127 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:22 - 2016-5-16 11:16:49 (26.633 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:49 - 2016-5-16 11:17:10 (20.929 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:10 (0.572 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:11 (0.253 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.000 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.661 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.158 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.126 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:20 (3.135 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:20 - 2016-5-16 11:17:46 (25.971 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21476
    Outputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:37:33 (19 minutes, 47.820 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21894
    Outputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:37:33 (0.041 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:37:33 (0.010 seconds)

    Branch 135

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0103_C.bam
    Commands
    Outputs
    • data/ubam/PN0103_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:53 (19.628 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0103_C.reverted.bam
    • data/ubam/PN0103_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0103_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.459 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0103_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0103_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.781 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0103_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.219 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.966 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.035 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.874 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.719 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.722 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.468 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.028 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.910 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 (0.836 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:37 (23.912 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21363
    Outputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:37 - 2016-5-16 11:22:37 (4 minutes, 59.726 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21565
    Outputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:22:37 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:22:37 (0.009 seconds)

    Branch 136

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0128_C.bam
    Commands
    Outputs
    • data/ubam/PN0128_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.292 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0128_C.reverted.bam
    • data/ubam/PN0128_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0128_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.866 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0128_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0128_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.658 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0128_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.118 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.360 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (24.708 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.662 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.680 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.630 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.783 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.910 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.855 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 (0.906 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (25.302 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21361
    Outputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:22:25 (4 minutes, 46.653 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21556
    Outputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:22:25 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:22:25 (0.008 seconds)

    Branch 137

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0133_C.bam
    Commands
    Outputs
    • data/ubam/PN0133_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.785 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0133_C.reverted.bam
    • data/ubam/PN0133_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0133_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.731 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0133_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0133_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.522 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0133_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.535 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:42 (22.845 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (25.187 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.612 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.553 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.680 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.061 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.689 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.049 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.757 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (24.853 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21416
    Outputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:38 - 2016-5-16 11:29:2 (11 minutes, 23.969 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21706
    Outputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:29:2 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:29:2 (0.008 seconds)

    Branch 138

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0118_C.bam
    Commands
    Outputs
    • data/ubam/PN0118_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.389 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0118_C.reverted.bam
    • data/ubam/PN0118_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0118_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.277 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0118_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0118_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.726 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0118_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.721 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.236 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.205 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:7 (0.525 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.759 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:8 (0.882 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.629 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.909 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.002 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 (0.823 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:40 (26.563 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21376
    Outputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:25:46 (8 minutes, 6.247 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21626
    Outputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:25:46 (0.038 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:25:46 (0.012 seconds)

    Branch 139

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0031_C.bam
    Commands
    Outputs
    • data/ubam/PN0031_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.623 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0031_C.reverted.bam
    • data/ubam/PN0031_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0031_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.494 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0031_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0031_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.451 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0031_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.356 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (23.868 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.719 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.446 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.600 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.648 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.858 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.890 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.022 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.783 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (27.316 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21423
    Outputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:30:49 (13 minutes, 7.799 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21741
    Outputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:30:49 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:30:49 (0.008 seconds)

    Branch 140

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0056_C.bam
    Commands
    Outputs
    • data/ubam/PN0056_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.155 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0056_C.reverted.bam
    • data/ubam/PN0056_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0056_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 (0.835 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0056_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0056_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.927 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0056_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.475 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.317 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.404 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.644 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.709 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.712 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.579 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.767 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:11 (0.882 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:12 (0.826 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:39 (25.458 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21391
    Outputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:39 - 2016-5-16 11:27:44 (10 minutes, 5.721 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21673
    Outputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:44 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:44 (0.008 seconds)

    Branch 141

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0154_C.bam
    Commands
    Outputs
    • data/ubam/PN0154_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.885 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0154_C.reverted.bam
    • data/ubam/PN0154_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0154_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.791 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0154_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0154_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:57 - 2016-5-16 11:16:18 (21.874 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0154_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.894 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (25.692 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.450 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.660 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.296 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.902 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.875 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.325 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.094 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.809 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (27.137 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21460
    Outputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:36:34 (18 minutes, 49.483 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21874
    Outputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:36:34 (0.047 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:36:34 (0.008 seconds)

    Branch 142

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0138_C.bam
    Commands
    Outputs
    • data/ubam/PN0138_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.229 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0138_C.reverted.bam
    • data/ubam/PN0138_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0138_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.258 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0138_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0138_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.752 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0138_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.443 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.427 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.984 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.778 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.688 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.993 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.722 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.489 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.352 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.356 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (27.446 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21457
    Outputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:35:0 (17 minutes, 15.681 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21847
    Outputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:35:0 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:35:0 (0.011 seconds)

    Branch 143

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0113_C.bam
    Commands
    Outputs
    • data/ubam/PN0113_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.857 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0113_C.reverted.bam
    • data/ubam/PN0113_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0113_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.825 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0113_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0113_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.734 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0113_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.408 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:47 (27.886 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.297 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.758 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.658 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.853 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.736 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:13 (0.881 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.143 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:19 (3.306 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:19 - 2016-5-16 11:17:46 (26.521 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21435
    Outputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:46 - 2016-5-16 11:33:18 (15 minutes, 32.290 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21808
    Outputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:33:18 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:33:18 (0.007 seconds)

    Branch 144

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0011_C.bam
    Commands
    Outputs
    • data/ubam/PN0011_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.552 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0011_C.reverted.bam
    • data/ubam/PN0011_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0011_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.147 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0011_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0011_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.899 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0011_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:21 (2.377 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:21 - 2016-5-16 11:16:44 (23.153 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.978 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.788 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.679 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.822 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.386 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.219 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.996 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.499 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (24.659 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21368
    Outputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:24:26 (6 minutes, 45.950 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21594
    Outputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:24:26 (0.035 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:24:26 (0.011 seconds)

    Branch 145

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0134_C.bam
    Commands
    Outputs
    • data/ubam/PN0134_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.060 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0134_C.reverted.bam
    • data/ubam/PN0134_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0134_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.980 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0134_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0134_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.847 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0134_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.950 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.928 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.484 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.710 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.637 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.784 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.787 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.387 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.028 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.483 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (25.368 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21384
    Outputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:26:6 (8 minutes, 25.224 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21637
    Outputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:26:6 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:26:6 (0.008 seconds)

    Branch 146

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0173_C.bam
    Commands
    Outputs
    • data/ubam/PN0173_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.792 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0173_C.reverted.bam
    • data/ubam/PN0173_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0173_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 (0.838 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0173_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0173_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.694 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0173_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.563 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.130 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.094 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.766 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.854 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.721 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.729 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.322 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.926 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.464 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (27.585 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21453
    Outputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:35:39 (17 minutes, 56.379 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21850
    Outputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:35:39 (0.036 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:35:39 (0.010 seconds)

    Branch 147

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0098_C.bam
    Commands
    Outputs
    • data/ubam/PN0098_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.941 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0098_C.reverted.bam
    • data/ubam/PN0098_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0098_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.123 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0098_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0098_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.109 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0098_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.960 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:48 (28.014 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:48 - 2016-5-16 11:17:9 (21.156 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.973 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:10 (0.468 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.606 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.829 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 (0.892 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.910 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:18 (2.220 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:18 - 2016-5-16 11:17:45 (27.394 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21428
    Outputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:45 - 2016-5-16 11:32:31 (14 minutes, 45.902 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21787
    Outputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:32:31 (0.036 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:32:31 (0.007 seconds)

    Branch 148

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0016_C.bam
    Commands
    Outputs
    • data/ubam/PN0016_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.569 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0016_C.reverted.bam
    • data/ubam/PN0016_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0016_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.220 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0016_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0016_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:19 (23.270 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0016_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.392 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (23.919 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.687 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.661 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.318 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.794 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.713 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.478 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.999 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.260 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.631 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21365
    Outputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:41 - 2016-5-16 11:22:56 (5 minutes, 15.232 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21571
    Outputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:22:56 (0.069 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:22:56 (0.009 seconds)

    Branch 149

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0114_C.bam
    Commands
    Outputs
    • data/ubam/PN0114_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.477 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0114_C.reverted.bam
    • data/ubam/PN0114_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0114_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.148 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0114_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0114_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.665 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0114_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 (0.711 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.623 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.270 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.758 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.738 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.916 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.398 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.991 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.912 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 (0.533 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.614 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21411
    Outputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:30:5 (12 minutes, 24.350 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21727
    Outputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:30:5 (0.040 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:30:5 (0.009 seconds)

    Branch 150

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0191_C.bam
    Commands
    Outputs
    • data/ubam/PN0191_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.917 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0191_C.reverted.bam
    • data/ubam/PN0191_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0191_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.119 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0191_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0191_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.898 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0191_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.323 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.755 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.055 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.818 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.352 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.742 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.921 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.027 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.027 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.673 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (27.851 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21436
    Outputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:44 - 2016-5-16 11:33:8 (15 minutes, 24.244 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21793
    Outputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:33:8 (0.034 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:33:8 (0.010 seconds)

    Branch 151

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0178_C.bam
    Commands
    Outputs
    • data/ubam/PN0178_C.reverted.bam
    Execution Time 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.991 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0178_C.reverted.bam
    • data/ubam/PN0178_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0178_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.299 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0178_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0178_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.693 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0178_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.449 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (26.171 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:45 - 2016-5-16 11:17:9 (23.237 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:9 (0.651 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:9 (0.689 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.579 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.096 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.050 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:13 (0.987 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.293 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (26.100 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21382
    Outputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:42 - 2016-5-16 11:27:7 (9 minutes, 25.595 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21652
    Outputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:27:7 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:27:7 (0.012 seconds)

    Branch 152

  1. makeUBAM

    Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.

    Inputs
    • ../Sanger/reorderedBams/PN0153_C.bam
    Commands
    Outputs
    • data/ubam/PN0153_C.reverted.bam
    Execution Time 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.623 seconds)
  2. fastqc_unmapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/ubam/PN0153_C.reverted.bam
    • data/ubam/PN0153_C.reverted.bam
    Commands
    Outputs
    • data/qc/PN0153_C.reverted_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.216 seconds)
  3. markAdapters

    Mark Illumina Adapters with PicardTools

    Inputs
    • data/qc/PN0153_C.reverted_fastqc.zip
    Commands
    Outputs
    • data/ubam/PN0153_C.reverted.markilluminaadapters.bam
    Execution Time 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.026 seconds)
  4. remapBWA

    Create merged BAM alignment from unmapped BAM file

    Inputs
    • data/ubam/PN0153_C.reverted.markilluminaadapters.bam
    Commands
    Outputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.bam
    Tools
    • bwa : 0.7.10-r789 - BWA is a software package for mapping low-divergent short read sequences against a large reference genome
    Execution Time 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.481 seconds)
  5. realignIntervals

    Inputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.bam
    Commands
    Outputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.intervals
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.041 seconds)
  6. realignIndels

    Inputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.intervals
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.intervals
    Commands
    Outputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.533 seconds)
  7. dedup

    Mark Duplicates with PicardTools

    Inputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.bam
    Commands
    Outputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Execution Time 2016-5-16 11:17:8 (0.873 seconds)
  8. bqsrPass1

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bam
    Commands
    Outputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Execution Time 2016-5-16 11:17:8 (0.657 seconds)
  9. bqsrPass2

    Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates

    Inputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.pass1.table
    Commands
    Outputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:9 (0.685 seconds)
  10. bqsrApply

    Apply BQSR to input BAM file.

    Inputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass2.pass2.table
    Commands
    Outputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:10 (0.870 seconds)
  11. bqsrCheck

    Compare pre and post base-quality scores from recalibration

    Inputs
    • data/aligned_bams/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.bam
    Commands
    Outputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:17:11 (0.842 seconds)
  12. fastqc_mapped

    Run FASTQC to generate QC metrics for the reads post-alignment

    Inputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrPass1.csv
    Commands
    Outputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Tools
    • fastqc : v0.11.3
    Execution Time 2016-5-16 11:17:12 (0.896 seconds)
  13. flagstat

    Inputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply_fastqc.zip
    Commands
    Outputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Tools
    • samtools : 1.2 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.273 seconds)
  14. alignment_metrics

    Collect alignment summary statistics

    Inputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.flagstat
    Commands
    Outputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Execution Time 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (25.876 seconds)
  15. insert_metrics

    Collect insert size metrics

    Inputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.alignment_metrics
    Commands21417
    Outputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Execution Time 2016-5-16 11:17:40 - 2016-5-16 11:31:11 (13 minutes, 30.869 seconds)
  16. depthOfCoverage

    Inputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.insert_metrics
    Commands21748
    Outputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:31:11 (0.033 seconds)
  17. callVariants

    Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf

    Inputs
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_statistics
    • data/qc/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.sample_summary
    Commands
    Outputs
    • data/variants/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Execution Time 2016-5-16 11:31:11 (0.007 seconds)

    Branch 153

  1. combineGVCF

    Jointly genotype gVCF files

    Inputs
    • data/variants/PN0003_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0004_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0005_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0006_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0007_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0008_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0009_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0010_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0011_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0012_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0013_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0014_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0015_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0016_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0019_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0020_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0022_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0023_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0025_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0027_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0028_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0029_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0030_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0031_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0032_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0035_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0037_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0040_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0041_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0042_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0043_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0044_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0054_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0055_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0055_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0056_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0057_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0058_Cx.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0059_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0063_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0073_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0074_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0075_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0077_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0078_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0079_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0081_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0082_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0083_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0084_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0085_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0086_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0087_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0089_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0090_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0091_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0097_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0098_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0099_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0101_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0102_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0103_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0104_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0105_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0107_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0108_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0109_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0110_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0111_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0112_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0113_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0114_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0115_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0116_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0117_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0118_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0119_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0120_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0121_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0122_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0124_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0125_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0126_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0127_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0128_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0129_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0130_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0131_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0133_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0134_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0135_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0138_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0140_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0141_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0142_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0143_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0145_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0148_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0149_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0150_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0151_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0153_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0154_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0155_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0156_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0157_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0159_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0160_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0161_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0162_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0163_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0164_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0165_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0166_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0167_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0168_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0169_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0170_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0171_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0172_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0173_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0176_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0177_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0178_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0179_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0180_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0181_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0182_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0183_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0184_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0185_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0186_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0187_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0188_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0189_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0190_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0191_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PN0192_C.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_DRS015A.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_DRS034.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XIA508.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XPA028.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUA001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUA011.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUA012.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUA020.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUA030.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUB001.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUC006.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUC009.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUC021.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    • data/variants/PNG_XUC022.reverted.markilluminaadapters.remapBWA.realignindels.dedup.bqsrApply.g.vcf
    Commands
    Outputs
    • data/variants_combined/combined_variants.vcf
    Execution Time 2016-5-16 11:40:20 (0.070 seconds)
  2. vqsrGenerate

    Generate variant quality score recalibration. Note requires GATK version 3.5

    Inputs
    • data/variants_combined/combined_variants.vcf
    Commands
    Outputs
    • data/variants_combined/combined_variants.vqsrGenerate.recal
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:40:20 (0.005 seconds)
  3. vqsrApply

    Apply variant quality score recalibration

    Inputs
    • data/variants_combined/combined_variants.vqsrGenerate.recal
    • data/variants_combined/combined_variants.vqsrGenerate.tranches
    • data/variants_combined/combined_variants.vqsrGenerate.plots.R
    Commands
    Outputs
    • data/variants_combined/combined_variants.vqsrApply.vcf
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:40:20 (0.004 seconds)
  4. annotate

    Annotate variants using snpEff

    Inputs
    • data/variants_combined/combined_variants.vqsrApply.vcf
    Commands21940
    Outputs
    • data/variants_combined/combined_variants.vqsrApply.annotate.vcf
    Execution Time 2016-5-16 11:40:20 - 2016-5-16 11:45:57 (5 minutes, 37.667 seconds)
  5. regions

    Include core regions from Pf genetic crosses version 1

    Inputs
    • data/variants_combined/combined_variants.vqsrApply.annotate.vcf
    Commands21941
    Outputs
    • data/variants_combined/combined_variants.vqsrApply.annotate.regions.vcf
    Execution Time 2016-5-16 11:45:57 - 2016-5-16 11:48:48 (2 minutes, 50.630 seconds)
  6. barcode

    Annotate global barcode SNPs from Neafsey et al., 2008

    Inputs
    • data/variants_combined/combined_variants.vqsrApply.annotate.regions.vcf
    Commands21942
    Outputs
    • data/variants_combined/combined_variants.vqsrApply.annotate.regions.barcode.vcf
    Execution Time 2016-5-16 11:48:48 - 2016-5-16 11:50:50 (2 minutes, 1.442 seconds)
  7. keepSNPs

    Kepp only SNPs in VCF file

    Inputs
    • data/variants_combined/combined_variants.vqsrApply.annotate.regions.barcode.vcf
    Commands21943
    Outputs
    • data/variants_combined/biallelic_only.vcf
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:50:50 - 2016-5-16 11:52:51 (2 minutes, 1.597 seconds)
  8. filterSNPs

    Annotate VCF file with additional filters at the variant level

    Inputs
    • data/variants_combined/biallelic_only.vcf
    • data/variants_combined/biallelic_only.vcf
    Commands21945
    Outputs
    • data/variants_combined/biallelic_only.filter.vcf
    Tools
    • GenomeAnalysisTK : 3.5-0-g36282e4 - A suite of tools for working with human medical resequencing projects
    Execution Time 2016-5-16 11:52:51 - 2016-5-16 11:53:27 (36.010 seconds)
  9. cleanVCF

    Clean VCF for analysis ready.

    Inputs
    • data/variants_combined/biallelic_only.filter.vcf
    • data/variants_combined/biallelic_only.filter.vcf
    Commands21947
    Outputs
    • cache/final_snps.vcf
    Execution Time 2016-5-16 11:53:27 - 2016-5-16 11:53:47 (20.183 seconds)
  10. extractAnno

    Use snpSift to extract annotations as plain text file

    Inputs
    • cache/final_snps.vcf
    • cache/final_snps.vcf
    Commands21949
    Outputs
    • cache/final_annotations.txt
    Execution Time 2016-5-16 11:53:47 - 2016-5-16 11:53:52 (4.831 seconds)
  11. indexVCF

    Inputs
    • cache/final_annotations.txt
    • cache/final_annotations.txt
    Commands21951
    Outputs
    • cache/final_annotations.txt
    Execution Time 2016-5-16 11:53:52 - 2016-5-16 11:57:26 (3 minutes, 33.700 seconds)
  12. cleanGDS

    Use clean VCF to construct GDS file

    Inputs
    • cache/final_annotations.txt
    • cache/final_annotations.txt
    Commands21952
    Outputs
    • cache/final_snps.cleanGDS.gds
    Execution Time 2016-5-16 11:57:26 - 2016-5-16 11:58:53 (1 minutes, 27.378 seconds)